Script | Spoken-Tutorial - User contributions [en]

LAMMPS-Molecular-Dynamics-Simulator/C2/Modeling-of-the-Single-Phase-System/English

2025-07-30T09:09:27Z

Snehalathak:

'''Title of script''': Modeling of the Single-Phase System

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi, Gopi Kundia

'''Keywords''': LAMMPS, Simulation video tutorial

{| border=1

|| '''Visual Cue '''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Modeling of the Single-Phase System.'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Set up a simulation of the bulk '''Lennard-Jones''' liquid.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| Use LAMMPS's '''''thermo_style''''' and '''''thermo''''' commands to extract and monitor properties such as;

temperature, potential energy, kinetic energy, total energy, density and pressure.

|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

Latest stable version of '''LAMMPS''' .
|-
|| '''Slide Number 4'''

'''Prerequisite'''
|| To follow this tutorial learner must be familiar with,

basic computer operations on '''Linux OS'''.

|-
|| '''Slide number 5'''

'''Code file'''
|| The following input file is required to practice this tutorial:

'''SPinputA.txt'''

This file is provided in the '''Code files''' link of this tutorial page.

|-
|| Open the input file SPinputAtxt in gedit test editor.
|| Here I have opened the input file '''SPinputA.txt''' in a text editor.

|-
|| Cursor on each section and highlight.
|| As described in the prerequisite tutorial, the input script is divided into four sections:

# '''Initialization'''
# '''System definition'''
# '''Simulation settings'''
# '''Running a simulation'''

|-
|| Cursor on the input file.
|| Please refer to the prerequisite tutorial for the details of the input commands for each section.

|-
|| Cursor on line 22: '''group liq type 1'''
|| Scroll down to the''' simulation settings '''section.

With this command all type 1 particles are grouped with a group ID '''liq.'''

|-
|| Scroll to '''Energy minimization '''section.

Cursor on lines 35 and 36,
|| Scroll to the '''Energy minimization '''section.

Here, we will use '''thermo_style '''and''' thermo '''commands.

'''thermo_style''' sets the style for printing thermodynamic data to the screen and log file.

The units for each column of output is determined by '''units''' command.

'''thermo''' command sets the frequency of printing thermodynamic data to the screen and log file.
|-
|| Line 34: '''timestep 0.005'''
||

The '''timestep''' command computes and prints the output at the mentioned time interval.

|-
|| Cursor on the line 52: '''fix 1 liq npt temp 0.8 0.8 0.5 iso 1 1 5'''
|| '''fix''' is any operation that is applied to the system during timestepping or minimization.

The '''npt''' command performs the time integration using equations of motion to generate positions and velocities for atoms.

In an '''np'''t ensemble, the number of particles, pressure and temperature of the system are held constant. 
|-
|| Cursor on the line 53: '''run 10000'''
|| Here 10,000 indicates the number of timesteps.

|-
|| '''Slide Number 6'''

'''About timestep command'''
|| About timestep command

We need to run the simulation long enough for the system to reach an equilibrium state.

This means its macroscopic properties like temperature, energy, density, and pressure have reached a stable plateau.

|-
|| '''Slide number 7'''

'''About timestep command'''
|| The values must be fluctuating around their average equilibrium values.

Once the system is stable, we can collect the data to study phenomena we are interested in.

We'll learn how to analyze these properties in the upcoming tutorial.

|-
|| Cursor on the input file.

Close the text editor.
|| Back to the input file.

Now let us run this input file.

Close the text editor.

|-
|| Go to the folder where the input file is located.

Open the folder and show the input file.

|| Navigate to the location of the input file.

|-
|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.

|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.

|-
|| Cursor on the terminal.
|| Alternatively, you can open the terminal and navigate to the path leading to the input file.
|-
|| At the prompt type '''lmp_serial -in SPinputA.txt'''

Press Enter.
|| Type the following command at the prompt to run the input file.

'''lmp_serial -in SPinputA.txt'''

Windows users can open the command prompt, type the command and proceed as shown.

Press Enter.
|-
|| Cursor on the terminal.

Open the folder containing the input file to show '''log.lammps''', '''thermo_properties.csv '''and '''output.atom.'''
|| The output is seen on the terminal.

Three output files are generated, '''log.lammps''', '''thermo_properties.csv''' and '''output.atom. '''

These files will be saved in the same folder where your input file is located.

|-
|| Cursor on the folder.
|| The analysis and visualization of the output files will be covered in the upcoming tutorial.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

Summary
|| Here is the summary for the tutorial.

|-
|| '''Slide Number 9'''

'''Assignment'''
|| As an assignment please do the following:

In the input script, modify the values for temperature.

Save and run the input file in LAMMPS.

|-
|| '''Slide Number 10'''

'''Acknowledgement'''
|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Modeling-of-the-Single-Phase-System/English

2025-07-29T09:22:48Z

Snehalathak: Created page with " '''Title of script''': Modeling of the Single-Phase System '''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi, Gopi Kundia '''Keywords''': LAMMPS, Simulation video tuto..."

'''Title of script''': Modeling of the Single-Phase System

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi, Gopi Kundia

'''Keywords''': LAMMPS, Simulation video tutorial

{| border=1

|| '''Visual Cue '''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Modeling of the Single-Phase System.'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Set up a simulation of the bulk '''Lennard-Jones''' liquid.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| Use LAMMPS's '''''thermo_style''''' and '''''thermo''''' commands to extract and monitor properties such as;

temperature, potential energy, kinetic energy, total energy, density and pressure.

|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

Latest stable version of '''LAMMPS''' .
|-
|| '''Slide Number 4'''

'''Prerequisite'''
|| To follow this tutorial learner must be familiar with,

basic computer operations on '''Linux OS'''.

|-
|| '''Slide number 5'''

'''Code file'''
|| The following input file is required to practice this tutorial:

'''SPinputA.txt'''

This file is provided in the '''Code files''' link of this tutorial page.

|-
|| Open the input file SPinputAtxt in gedit test editor.
|| Here I have opened the input file '''SPinputA.txt''' in a text editor.

|-
|| Cursor on each section and highlight.
|| As described in the prerequisite tutorial, the input script is divided into four sections:

# '''Initialization'''
# '''System definition'''
# '''Simulation settings'''
# '''Running a simulation'''

|-
|| Cursor on the input file.
|| Please refer to the prerequisite tutorial for the details of the input commands for each section.

|-
|| Cursor on line 22: '''group liq type 1'''
|| Scroll down to the''' simulation settings '''section.

With this command all type 1 particles are grouped with a group ID '''liq.'''

|-
|| Scroll to '''Energy minimization '''section.

Cursor on lines 35 and 36,
|| Scroll to the '''Energy minimization '''section.

Here, we will use '''thermo_style '''and''' thermo '''commands.

'''thermo_style''' sets the style for printing thermodynamic data to the screen and log file.

The units for each column of output is determined by '''units''' command.

'''thermo''' command sets the frequency of printing thermodynamic data to the screen and log file.
|-
|| Line 34: '''timestep 0.005'''
||

The '''timestep''' command computes and prints the output at the mentioned time interval.

|-
|| Cursor on the line 52: '''fix 1 liq npt temp 0.8 0.8 0.5 iso 1 1 5'''
|| '''fix''' is any operation that is applied to the system during timestepping or minimization.

The '''npt''' command performs the time integration using equations of motion to generate positions and velocities for atoms.

In an '''np'''t ensemble, the number of particles, pressure and temperature of the system are held constant. 
|-
|| Cursor on the line 53: '''run 10000'''
|| Here 10,000 indicates the number of timesteps.

|-
|| '''Slide Number 6'''

'''About timestep command'''
|| About timestep command

We need to run the simulation long enough for the system to reach an equilibrium state.

This means its macroscopic properties like temperature, energy, density, and pressure have reached a stable plateau.

|-
|| '''Slide number 7'''

'''About timestep command'''
|| The values must be fluctuating around their average equilibrium values.

Once the system is stable, we can collect the data to study phenomena we are interested in.

We'll learn how to analyze these properties in the upcoming tutorial.

|-
|| Cursor on the input file.

Close the text editor.
|| Back to the input file.

Now let us run this input file.

Close the text editor.

|-
|| Go to the folder where the input file is located.

Open the folder and show the input file.

|| Navigate to the location of the input file.

|-
|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.

|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.

|-
|| Cursor on the terminal.
|| Alternatively you can open the terminal and navigate to the path leading to the input file.
|-
|| At the prompt type '''lmp_serial -in SPinputA.txt'''

Press Enter.
|| Type the following command at the prompt to run the input file.

'''lmp_serial -in SPinputA.txt'''

Windows users can open the command prompt, type the command and proceed as shown.

Press Enter.
|-
|| Cursor on the terminal.

Open the folder containing the input file to show '''log.lammps''', '''thermo_properties.csv '''and '''output.atom.'''
|| The output is seen on the terminal.

Three output files are generated, '''log.lammps''', '''thermo_properties.csv''' and '''output.atom. '''

These files will be saved in the same folder where your input file is located.

|-
|| Cursor on the folder.
|| The analysis and visualization of the output files will be covered in the upcoming tutorial.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

Summary
|| Here is the summary for the tutorial.

|-
|| '''Slide Number 9'''

'''Assignment'''
|| As an assignment please do the following:

In the input script, modify the values for temperature.

Save and run the input file in LAMMPS.

|-
|| '''Slide Number 10'''

'''Acknowledgement'''
|| Thank you
|-
|}

ORCA---Computational-Chemistry/C2/Generate--Molecular-Orbitals-of-Water/English

2025-07-25T07:36:21Z

Snehalathak:

'''Title of the script''': '''Generate Molecular Orbitals of Water'''

'''Author: '''Madhuri Ganapathi, Raj Singh, Snehalatha Kaliappan

'''Keywords''': orca, molecular orbitals of water, gedit text editor, auto optimization, molecular orbitals, homo, lumo, ucsf chimera, computational chemistry, video tutorial.

{|border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1 '''

'''Title slide '''
|| Welcome to the Spoken tutorial on '''Generate Molecular Orbitals of Water'''.
|-
|| '''Slide Number 2 '''

'''Learning Objectives'''

|| In this tutorial, we will learn to,
* Open the XYZ file.
* Add commands to create the input file.
* Run the input file in ORCA environment to get the ORCA output.
* View the molecular orbital data in the output file.

|-
|| '''Slide Number 3'''

'''System Requirements'''
|| To record this tutorial, I am using;
* '''Ubuntu Linux OS '''version 22.04
* '''ORCA '''version 6.0.1
* '''Gedit Text Editor''' version 41.0

Windows users may use notepad or any other text editor.

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

|| To follow this tutorial, learners should be familiar with '''ORCA software'''.

|-
|| '''Slide Number 5'''

'''Code Files'''

The following code file is required to practice this tutorial

1.'''water.xyz'''

2. '''commands.txt'''

These files are provided in the Code Files link of this tutorial page

|| The following code files are required to practice this tutorial.

These files are provided in the Code Files link of this tutorial page.
|-
|| Show the downloaded and extracted file to Home directory
|| Download and extract '''water''' folder from the '''Code files''' link to the '''Home directory'''.
|-
|| Right-click on the file

From the context menu select Open With Text Editor.
|| Let us open the '''water.xyz '''file using a text editor.
|-
|| Select and Delete 3 from the first row.

Press Ctrl+ S to save the file.
|| Delete 3 from the first row and save the file.
|-
|| Right-click on the commands.txt file and '''Open With Text Editor'''
|| Now we will open '''commands.txt''' file using a text editor.

|-
|| Copy the commands(Ctrl+ C)

Paste in the water.xyz(Ctrl+V)

|| Copy and paste the commands from the file in the first row of the '''water.xyz '''file.

|-
|| Type * at the end of the coordinates.
|| At the end of the coordinates row type an '''asterisk''' (*)

We will now go through the code.
|-
|| '''! B3LYP def2-SVP TightSCF Opt'''

'''Highlight !'''

'''Highlight B3LYP'''

'''! B3LYP def2-SVP '''

'''Highlight def2-SVP'''

'''Highlight TightSCF Opt'''
|| The command line starts with an exclamation mark.

Here '''B3LYP''' is the''' dft functional'''.

'''def2-SVP '''is the''' basis set'''.

'''TightSCF Opt''' is the command for geometry optimization.
|-
|| '''%output'''

'''Print[P_MOs] 1'''

'''end'''

|| This block of code is used to print the molecular orbitals of water.

|-
|| Point to * xyz 0 1

*

Point to the asterisk at the start and end.

|| Here '''xyz '''specifies the coordinates of the molecule.

0 is the charge and 1 is the spin multiplicity.

The coordinates start and end with an '''asterisk''' (*).
|-
|| Point to the numbers and xyz coordinates.

Highlight the xyz coordinates.

Point to the entire code.
|| The numbers in rows are the '''xyz''' coordinates of the atoms in '''Angstrom '''units.

This is the ORCA input file for generating molecular orbitals of water.

|-
|| Click on the '''3 lines''' icon next '''Save''' button.

In the drop down menu select '''Save As '''option.

Delete '''.xyz '''and '''.inp '''as the extension.

In the '''Save '''dialog box type the file name as '''water.inp'''.

Choose location as '''water folder'''.

Click on the '''Save''' button.

|| Let us now save the file as an input file.

Click on the 3 lines icon next to the '''Save '''button.

In the drop down menu select '''Save As '''option.

In the '''Save''' dialog box type the file name as '''water.inp'''.

Choose the '''water''' folder to save the file.

Click the '''Save''' button.

|-
|| Open the''' Home''' directory

Open the water folder by double clicking on it.
|| Let us go to the '''Home''' directory and open the''' water '''folder.

It contains the '''water.inp''' file.
|-
|| To open the terminal in water folder,

Right-click and from the context menu

select Open in Terminal.
|| Let us now open the terminal in '''water '''folder.

Right-click and from the context menu

select '''Open in Terminal'''.

|-
|| type at the prompt''' file water.inp'''

point to the output

'''water.inp: Unicode text, UTF-8 (with BOM) text '''
|| To check the file format of '''water.inp,''' at the prompt''' '''type''' file water.inp'''

Press''' Enter'''.

'''Terminal '''shows the below output.

If the''' terminal '''shows '''water.inp: ASCII text '''as output, please skip the following steps.

|-
|| Copy paste the command at the prompt

'''sed -i '1s/^\xEF\xBB\xBF//' water.inp'''

'''Press Ctrl + Shift +V to paste in the terminal'''

Press Enter.
|| We need to convert the Unicode text to '''ASCII'''

text as '''ORCA '''reads only the '''ASCII''' text file.

Let’s open the '''commands.txt''' file again.

Copy and paste the command from commands.txt file to the terminal.

Press Enter
|-
|| Type '''file water.inp'''

Point to the output.

'''water.inp: ASCII text'''

|| To check the file format of '''water.inp''' at the prompt''' '''type '''file water.inp'''

This time terminal shows the below output.
Now let us run the input file in ORCA.

|-
|| Type '''orca water.inp > water.out'''

Press Enter
|| Type '''orca space water.inp space > space water.out'''

Here a greater than('''>''') sign is used to channel the output to the same folder.

Press''' Enter'''.
|-
|| Point to files in the water folder, in the HOME directory
|| After the calculation is complete the output file '''water.out''' is generated.

The output file is available in the '''water''' folder in the '''HOME''' directory.

|-
|| Type

'''less water.out'''

The .out file opens on the terminal and then press “/” and write in capital “'''ORBITAL ENERGIES'''” and press “Enter”.

|| At the prompt type '''less space water.out'''.

The '''.out''' file opens on the terminal.

Now let us search for the keyword '''ORBITAL ENERGIES.'''

At the colon prompt on the terminal,

Press back slash (/) and then type in capital letters '''ORBITAL ENERGIES'''.

Press Enter.

|-
|| The Orbital energies Table will appear.

point to the table.

|| The orbital energies table is displayed on the terminal.

|-
|| '''highlight the Second column''' which tells about the population and '''the first column''' which tells about the Orbital Number.

point to the second column.

point to orbital 4 and its population.

|| In this table, look at the second column.

It tells us about the population of the orbitals.

Note that for the water molecule the highest occupied orbital number 4 has least energy.

It has the last highest population of 2.0000.

Number 4 orbital is HOMO.

|-
|| point to orbital 5 and its population.
|| Now observe orbital number 5.

It has the first least population and least energy among the unoccupied orbitals.

Number 5 orbital is LUMO.

|-
|| point to HOMO and LUMO
|| We will visualize HOMO and LUMO orbitals using Chimera in the upcoming tutorial.

|-
|| Only Narration
|| Please refer to the additional reading material to learn more about the molecular orbitals of water.
|-

|| With this we come to the end of this tutorial.
|-
|| '''Slide Number 6'''

'''Summary'''

In this tutorial, we have learnt to,

* Open the XYZ file.
* Add commands to create the input file.
* Run the input file in '''ORCA''' environment to get the '''ORCA''' Output.
* View molecular orbital data in the output file.

|| Let us summarize.
|-
|| '''Slide Number 7'''

'''Assignment '''

* Create '''ORCA''' input files for carbon monoxide and ammonia.
* Run the''' '''input files in '''ORCA''' environment using the terminal to generate the output files.
* View HOMO and LUMO orbital data in the output files.

|| As an assignment please do the following.

|-
||
|| Thank you for joining.
|-
|}

ORCA---Computational-Chemistry/C2/Generate--Molecular-Orbitals-of-Water/English

2025-07-23T10:54:43Z

Snehalathak: Created page with " '''Title of the script''': Generate Molecular Orbitals of Water using ORCA 6.0.1 '''Author: '''Madhuri Ganapathi, Raj Singh, Snehalatha Kaliappan '''Keywords:''' Gedit tex..."

'''Title of the script''': Generate Molecular Orbitals of Water using ORCA 6.0.1

'''Author: '''Madhuri Ganapathi, Raj Singh, Snehalatha Kaliappan

'''Keywords:''' Gedit text editor, auto optimization, Molecular orbitals, HOMO, LUMO, video tutorial.

{|border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1 '''

'''Title slide '''
|| Welcome to the Spoken tutorial on '''Generate Molecular Orbitals of Water'''.
|-
|| '''Slide Number 2 '''

'''Learning Objectives'''

|| In this tutorial, we will learn to,
* Open the XYZ file.
* Add commands to create the input file.
* Run the input file in ORCA environment to get the ORCA output.
* View the molecular orbital data in the output file.

|-
|| '''Slide Number 3'''

'''System Requirements'''
|| To record this tutorial, I am using;
* '''Ubuntu Linux OS '''version 22.04
* '''ORCA '''version 6.0.1
* '''Gedit Text Editor''' version 41.0

Windows users may use notepad or any other text editor.

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

|| To follow this tutorial, learners should be familiar with '''ORCA software'''.

|-
|| '''Slide Number 5'''

'''Code Files'''

The following code file is required to practice this tutorial

1.'''water.xyz'''

2. '''commands.txt'''

These files are provided in the Code Files link of this tutorial page

|| The following code files are required to practice this tutorial.

These files are provided in the Code Files link of this tutorial page.
|-
|| Show the downloaded and extracted file to Home directory
|| Download and extract '''water''' folder from the '''Code files''' link to the '''Home directory'''.
|-
|| Right-click on the file

From the context menu select Open With Text Editor.
|| Let us open the '''water.xyz '''file using a text editor.
|-
|| Select and Delete 3 from the first row.

Press Ctrl+ S to save the file.
|| Delete 3 from the first row and save the file.
|-
|| Right-click on the commands.txt file and '''Open With Text Editor'''
|| Now we will open '''commands.txt''' file using a text editor.

|-
|| Copy the commands(Ctrl+ C)

Paste in the water.xyz(Ctrl+V)

|| Copy and paste the commands from the file in the first row of the '''water.xyz '''file.

|-
|| Type * at the end of the coordinates.
|| At the end of the coordinates row type an '''asterisk''' (*)

We will now go through the code.
|-
|| '''! B3LYP def2-SVP TightSCF Opt'''

'''Highlight !'''

'''Highlight B3LYP'''

'''! B3LYP def2-SVP '''

'''Highlight def2-SVP'''

'''Highlight TightSCF Opt'''
|| The command line starts with an exclamation mark.

Here '''B3LYP''' is the''' dft functional'''.

'''def2-SVP '''is the''' basis set'''.

'''TightSCF Opt''' is the command for geometry optimization.
|-
|| '''%output'''

'''Print[P_MOs] 1'''

'''end'''

|| This block of code is used to print the molecular orbitals of water.

|-
|| Point to * xyz 0 1

*

Point to the asterisk at the start and end.

|| Here '''xyz '''specifies the coordinates of the molecule.

0 is the charge and 1 is the spin multiplicity.

The coordinates start and end with an '''asterisk''' (*).
|-
|| Point to the numbers and xyz coordinates.

Highlight the xyz coordinates.

Point to the entire code.
|| The numbers in rows are the '''xyz''' coordinates of the atoms in '''Angstrom '''units.

This is the ORCA input file for generating molecular orbitals of water.

|-
|| Click on the '''3 lines''' icon next '''Save''' button.

In the drop down menu select '''Save As '''option.

Delete '''.xyz '''and '''.inp '''as the extension.

In the '''Save '''dialog box type the file name as '''water.inp'''.

Choose location as '''water folder'''.

Click on the '''Save''' button.

|| Let us now save the file as an input file.

Click on the 3 lines icon next to the '''Save '''button.

In the drop down menu select '''Save As '''option.

In the '''Save''' dialog box type the file name as '''water.inp'''.

Choose the '''water''' folder to save the file.

Click the '''Save''' button.

|-
|| Open the''' Home''' directory

Open the water folder by double clicking on it.
|| Let us go to the '''Home''' directory and open the''' water '''folder.

It contains the '''water.inp''' file.
|-
|| To open the terminal in water folder,

Right-click and from the context menu

select Open in Terminal.
|| Let us now open the terminal in '''water '''folder.

Right-click and from the context menu

select '''Open in Terminal'''.

|-
|| type at the prompt''' file water.inp'''

point to the output

'''water.inp: Unicode text, UTF-8 (with BOM) text '''
|| To check the file format of '''water.inp,''' at the prompt''' '''type''' file water.inp'''

Press''' Enter'''.

'''Terminal '''shows the below output.

If the''' terminal '''shows '''water.inp: ASCII text '''as output, please skip the following steps.

|-
|| Copy paste the command at the prompt

'''sed -i '1s/^\xEF\xBB\xBF//' water.inp'''

'''Press Ctrl + Shift +V to paste in the terminal'''

Press Enter.
|| We need to convert the Unicode text to '''ASCII'''

text as '''ORCA '''reads only the '''ASCII''' text file.

Let’s open the '''commands.txt''' file again.

Copy and paste the command from commands.txt file to the terminal.

Press Enter
|-
|| Type '''file water.inp'''

Point to the output.

'''water.inp: ASCII text'''

|| To check the file format of '''water.inp''' at the prompt''' '''type '''file water.inp'''

This time terminal shows the below output.
|-
|| Now let us run the input file in ORCA.

|-
|| Type '''orca water.inp > water.out'''

Press Enter
|| Type '''orca space water.inp space > space water.out'''

Here a greater''' '''than('''>''') sign is used to channel the output to the same folder.

Press''' Enter'''.
|-
|| Point to files in the water folder, in the HOME directory
|| After the calculation is complete the output file '''water.out''' is generated.

The output file is available in the '''water''' folder in the '''HOME''' directory.

|-
|| Type

'''less water.out'''

The .out file opens on the terminal and then press “/” and write in capital “'''ORBITAL ENERGIES'''” and press “Enter”.

|| At the prompt type '''less space water.out'''.

The '''.out''' file opens on the terminal.

Now let us search for the keyword '''ORBITAL ENERGIES.'''

At the colon prompt on the terminal,

Press back slash (/) and then type in capital letters '''ORBITAL ENERGIES'''.

Press Enter.

|-
|| The Orbital energies Table will appear.

point to the table.

|| The orbital energies table is displayed on the terminal.

|-
|| '''highlight the Second column''' which tells about the population and '''the first column''' which tells about the Orbital Number.

point to the second column.

point to orbital 4 and its population.

|| In this table, look at the second column.

It tells us about the population of the orbitals.

Note that for the water molecule the highest occupied orbital number 4 has least energy.

It has the last highest population of 2.0000.

Number 4 orbital is HOMO.

|-
|| point to orbital 5 and its population.

|| Now observe orbital number 5.

It has the first least population and least energy among the unoccupied orbitals.

Number 5 orbital is LUMO.

|-
|| point to HOMO and LUMO
|| We will visualize HOMO and LUMO orbitals using Chimera in the upcoming tutorial.

|-
|| Only Narration
|| Please refer to the additional reading material to learn more about the molecular orbitals of water.
|-

|| With this we come to the end of this tutorial.
|-
|| '''Slide Number 6'''

'''Summary'''

In this tutorial, we have learnt to,

* Open the XYZ file.
* Add commands to create the input file.
* Run the input file in '''ORCA''' environment to get the '''ORCA''' Output.
* View molecular orbital data in the output file.

|| Let us summarize.
|-
|| '''Slide Number 7'''

'''Assignment '''

* Create '''ORCA''' input files for carbon monoxide and ammonia.
* Run the''' '''input files in '''ORCA''' environment using the terminal to generate the output files.
* View HOMO and LUMO orbital data in the output files.

|| As an assignment please do the following.

|-
||
|| Thank you for joining.
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Visualizing-the-LAMMPS-Output-using-OVITO/English

2025-07-14T11:56:40Z

Snehalathak:

'''Title of script''': Visualizing the LAMMPS Output using OVITO

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, installation of OVITO, download OVIT, visualize lammps output , video tutorial

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Visualizing the LAMMPS Output using OVITO'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''OVITO''' open visualization tool.

Visualize the LAMMPS output file in '''OVITO'''.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

'''OVITO basic''' version 3.12.4
|-
|| '''Slide number 4'''

'''Code file'''
|| The following input file is required to practice this tutorial:

'''LJoutput1.atom'''

This file is provided in the '''Code files''' link of this tutorial page.
|-
|| '''Slide number 5'''

About OVITO

https://www.ovito.org/
|| '''OVITO''' - Open Visualization Tool.

It is used for Scientific data visualization and analysis solution for particle-based simulations.

'''OVITO Basic''' is available free of charge under an open source license.
|-
|| Type ovito.org and press enter.
|| Open any web browser and type ovito.org and press Enter.
|-
|| click on the Download button at the center of the page.
|| The web page opens.

Click on the '''Download''' button at the center of the page.
|-
|| Cursor on the various buttons.

click on Linux button.
|| You will see buttons for downloading installer files for various OS.

User can choose the appropriate button depending on the OS being used.

I will click on '''Linux''' button.
|-
|| Cursor on the options.

Click on OVITO basic button.
|| You will see two options, '''OVITO Basic''' and '''OVITOPro'''.

Click on''' OVITO basic''' button.

The installer files download to you '''Downloads''' directory.
|-
|| Click on the '''Installation Instruction''' link.

Cursor on the
|| Click on the '''Installations Instruction''' link given in the middle of the page.

'''Installation''' page opens with detailed information on how to install OVITO on various OS.
|-
|| Open the '''Downloads''' folder and locate the compressed  '''ovito-basic-3.12.4-x86_64.tar.xz'''tar.xz file

Right-click on the file and choose '''Extract Here''' option.
|| Open the '''Downloads''' folder and locate the compressed '''tar.xz''' file.

Right-click on the file and choose '''Extract Here''' option.
|-
|| Double-click on the extracted folder.

Double-click on the '''bin '''folder.
|| Double-click on the extracted folder to open it.

Double-click on the '''bin '''folder.

The folder opens.
|-
|| Double-click on '''ovito.'''
|| Double-click on '''ovito.'''

'''OVITO''' interface opens.
|-
|| Click on '''File''' menu, from the sub-menu click on '''Load File''' option.
|| Click on '''File''' menu, from the sub-menu click on the '''Load File''' option.
|-
|| Cursor on '''Load File''' pop up box.
|| '''Load File''' pop up box opens.

Navigate to the location of the lammps output file for LJ bulk liquid simulation.
|-
|| Select the LJoutput1.atom from the list and click on open button at the bottom-right corner.
|| Select the '''LJoutput1.atom''' from the list and click on''' open '''button at the bottom-right corner.
|-
|| Cursor on the panel.
|| The simulation of the '''Lennard Jones bulk liqiud''' opens.

The views from various viewing angles is seen on the panel.
|-
|| Click on the image with the mouse and rotate,
|| Use the mouse to rotate the images on the panel.
|-
|| On the right-side panel click on the '''Particle Types'''
|| On the right-side panel click on the '''Particle Types '''under''' Data Source.'''
|-
|| Particle Types panel opens on the right panel.

In the Appearance section, input the '''Display radius''' as 0.5
|| Particle Types panel opens on the right panel.

In the '''Appearance''' section, input the '''Display radius''' as 0.5.

This will allow proper rendering of the particles.
|-
|| Cursor on the panel.
|| We will learn to use more features of '''OVITO''' in the upcoming tutorials.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 6'''

Summary
|| Let's summarize.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment please do the following:

Explore the various various options to change the appearance of the particles.
|-
|| '''Slide Number 8'''
|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Visualizing-the-LAMMPS-Output-using-OVITO/English

2025-07-14T11:55:20Z

Snehalathak:

'''Title of script''': Visualizing the LAMMPS Output using OVITO

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, installation of OVITO, download OVIT, visualize lammps output , video tutorial

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Visualizing the LAMMPS Output using OVITO'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''OVITO''' open visualization tool.

Visualize the LAMMPS output file in '''OVITO'''.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

'''OVITO basic''' version 3.12.4
|-
|| '''Slide number 4'''

'''Code file'''
|| The following input file is required to practice this tutorial:

'''LJoutput1.atom'''

This file is provided in the '''Code files''' link of this tutorial page.
|-
|| '''Slide number 5'''

About OVITO

https://www.ovito.org/
|| '''OVITO''' - Open Visualization Tool.

It is used for Scientific data visualization and analysis solution for particle-based simulations.

'''OVITO Basic''' is available free of charge under an open source license.
|-
|| Type ovito.org and press enter.
|| Open any web browser and type ovito.org and press Enter.
|-
|| click on the Download button at the center of the page.
|| The web page opens.

Click on the '''Download''' button at the center of the page.
|-
|| Cursor on the various buttons.

click on Linux button.
|| You will see buttons for downloading installer files for various OS.

User can choose the appropriate button depending on the OS being used.

I will click on '''Linux''' button.
|-
|| Cursor on the options.

Click on OVITO basic button.
|| You will see two options, '''OVITO Basic''' and '''OVITOPro'''.

Click on''' OVITO basic''' button.

The installer files download to you '''Downloads''' directory.
|-
|| Click on the '''Installation Instruction''' link.

Cursor on the
|| Click on the '''Installations Instruction''' link given in the middle of the page.

'''Installation''' page opens with detailed information on how to install OVITO on various OS.
|-
|| Open the '''Downloads''' folder and locate the compressed  '''ovito-basic-3.12.4-x86_64.tar.xz'''tar.xz file

Right-click on the file and choose '''Extract Here''' option.
|| Open the '''Downloads''' folder and locate the compressed '''tar.xz''' file.

Right-click on the file and choose '''Extract Here''' option.
|-
|| Double-click on the extracted folder.

Double-click on the '''bin '''folder.
|| Double-click on the extracted folder to open it.

Double-click on the '''bin '''folder.

The folder opens.
|-
|| Double-click on '''ovito.'''
|| Double-click on '''ovito.'''

'''OVITO''' interface opens.
|-
|| Click on '''File''' menu, from the sub-menu click on '''Load File''' option.
|| Click on '''File''' menu, from the sub-menu click on the '''Load File''' option.
|-
|| Cursor on '''Load File''' pop up box.
|| '''Load File''' pop up box opens.

Navigate to the location of the lammps out put file for LJ bulk liquid simulation.
|-
|| Select the LJoutput1.atom from the list and click on open button at the bottom-right corner.
|| Select the '''LJoutput1.atom''' from the list and click on''' open '''button at the bottom-right corner.
|-
|| Cursor on the panel.
|| The simulation of the L'''ennard Jones bulk liqiud''' opens.

The views from various viewing angles is seen on the panel.
|-
|| Click on the image with the mouse and rotate,
|| Use the mouse to rotate the images on the panel.
|-
|| On the right-side panel click on the '''Particle Types'''
|| On the right-side panel click on the '''Particle Types '''under''' Data Source.'''
|-
|| Particle Types panel opens on the right panel.

In the Appearance section, input the '''Display radius''' as 0.5
|| Particle Types panel opens on the right panel.

In the '''Appearance''' section, input the '''Display radius''' as 0.5.

This will allow proper rendering of the particles.
|-
|| Cursor on the panel.
|| We will learn to use more features of '''OVITO''' in the upcoming tutorials.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 6'''

Summary
|| Let's summarize.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment please do the following:

Explore the various various options to change the appearance of the particles.
|-
|| '''Slide Number 8'''
|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Visualizing-the-LAMMPS-Output-using-OVITO/English

2025-07-14T11:54:27Z

Snehalathak:

'''Title of script''': Visualizing the LAMMPS Output using OVITO

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, installation of OVITO, download OVIT, visualize lammps output , video tutorial

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Visualizing the LAMMPS Output using OVITO'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''OVITO''' open visualization tool.

Visualize the LAMMPS output file in '''OVITO'''.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

'''OVITO basic''' version 3.12.4
|-
|| '''Slide number 4'''

'''Code file'''
|| The following input file is required to practice this tutorial:

'''LJoutput1.atom'''

This file is provided in the '''Code files''' link of this tutorial page.
|-
|| '''Slide number 5'''

About OVITO

https://www.ovito.org/
|| '''OVITO''' - Open Visualization Tool.

It is used for Scientific data visualization and analysis solution for particle-based simulations.

'''OVITO Basic''' is available free of charge under an open source license.
|-
|| Type ovito.org and press enter.
|| Open any web browser and type ovito.org and press Enter.
|-
|| click on the Download button at the center of the page.
|| The web page opens.

Click on the '''Download''' button at the center of the page.
|-
|| Cursor on the various buttons.

click on Linux button.
|| You will see buttons for downloading installer files for various OS.

User can choose the appropriate button depending on the OS being used.

I will click on '''Linux''' button.
|-
|| Cursor on the options.

Click on OVITO basic button.
|| You will see two options, '''OVITO Basic''' and '''OVITOPro'''.

Click on''' OVITO basic''' button.

The installer files download to you '''Downloads''' directory.
|-
|| Click on the '''Installations Instruction''' link.

Cursor on the
|| Click on the '''Installations Instruction''' link given in the middle of the page.

'''Installation''' page opens with detailed information on how to install OVITO on various OS.
|-
|| Open the '''Downloads''' folder and locate the compressed  '''ovito-basic-3.12.4-x86_64.tar.xz'''tar.xz file

Right-click on the file and choose '''Extract Here''' option.
|| Open the '''Downloads''' folder and locate the compressed '''tar.xz''' file.

Right-click on the file and choose '''Extract Here''' option.
|-
|| Double-click on the extracted folder.

Double-click on the '''bin '''folder.
|| Double-click on the extracted folder to open it.

Double-click on the '''bin '''folder.

The folder opens.
|-
|| Double-click on '''ovito.'''
|| Double-click on '''ovito.'''

'''OVITO''' interface opens.
|-
|| Click on '''File''' menu, from the sub-menu click on '''Load File''' option.
|| Click on '''File''' menu, from the sub-menu click on the '''Load File''' option.
|-
|| Cursor on '''Load File''' pop up box.
|| '''Load File''' pop up box opens.

Navigate to the location of the lammps out put file for LJ bulk liquid simulation.
|-
|| Select the LJoutput1.atom from the list and click on open button at the bottom-right corner.
|| Select the '''LJoutput1.atom''' from the list and click on''' open '''button at the bottom-right corner.
|-
|| Cursor on the panel.
|| The simulation of the L'''ennard Jones bulk liqiud''' opens.

The views from various viewing angles is seen on the panel.
|-
|| Click on the image with the mouse and rotate,
|| Use the mouse to rotate the images on the panel.
|-
|| On the right-side panel click on the '''Particle Types'''
|| On the right-side panel click on the '''Particle Types '''under''' Data Source.'''
|-
|| Particle Types panel opens on the right panel.

In the Appearance section, input the '''Display radius''' as 0.5
|| Particle Types panel opens on the right panel.

In the '''Appearance''' section, input the '''Display radius''' as 0.5.

This will allow proper rendering of the particles.
|-
|| Cursor on the panel.
|| We will learn to use more features of '''OVITO''' in the upcoming tutorials.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 6'''

Summary
|| Let's summarize.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment please do the following:

Explore the various various options to change the appearance of the particles.
|-
|| '''Slide Number 8'''
|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Visualizing-the-LAMMPS-Output-using-OVITO/English

2025-07-11T08:26:31Z

Snehalathak:

'''Title of script''': Visualizing the LAMMPS Output using OVITO

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, installation of OVITO, download OVIT, visualize lammps output , video tutorial

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Visualizing the LAMMPS Output using OVITO'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''OVITO''' open visualization tool

Visualize the LAMMPS output file in '''OVITO'''.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

'''OVITO basic''' version 3.12.4
|-
|| '''Slide number 4'''

'''Code file'''
|| The following input file is required to practice this tutorial:

'''LJoutput1.atom'''

This file is provided in the Code files link of this tutorial page.
|-
|| '''Slide number 5'''

About OVITO

https://www.ovito.org/
|| '''OVITO''' is an Open Visualization Tool

It is used for Scientific data visualization and analysis solution for particle-based simulations

'''OVITO Basic''' is available free of charge under an open source license.
|-
|| Type ovito.org and press enter.
|| Open any web browser and type ovito.org and press enter.
|-
|| click on the Download button at the center of the page.
|| The web page opens, click on the '''Download''' button at the center of the page.
|-
|| Cursor on the various buttons.

click on Linux button.
|| You will see buttons for downloading installer files for various OS.

User can choose the appropriate button depending on the OS being used.

I will click on Linux button.
|-
|| Cursor on the options.

Click on OVITO basic button.
|| You will see two options, '''OVITO Basic''' and '''OVITOPro'''.

Click on''' OVITO basic''' button.

The installer files download to you downloads directory.
|-
|| Click on the '''Installations Instruction''' link.

Cursor on the
|| Click on the '''Installations Instruction''' link given in the middle of the page.

'''Installation''' page opens with detailed information on how to install OVITO on various OS.
|-
|| Open the '''Downloads''' folder and locate the compressed  '''ovito-basic-3.12.4-x86_64.tar.xz'''tar.xz file

Right-click on the file and choose '''Extract Here''' option.
|| Open the '''Downloads''' folder and locate the compressed tar.xz file.

Right-click on the file and choose '''Extract Here''' option.
|-
|| Double-click on the extracted folder.

Double-click on the '''bin '''folder.
|| Double-click on the extracted folder to open it.

Double-click on the '''bin '''folder. The folder opens.
|-
|| Double-click on '''ovito.'''
|| The folder opens, Double-click on '''ovito.'''

'''OVITO''' interface opens.
|-
|| Click on '''File''' menu, from the sub-menu click on '''Load File''' option.
|| Click on '''File''' menu, from the sub-menu click on

'''Load File''' option.
|-
|| Cursor on '''Load File''' pop up box.
|| '''Load File''' pop up box opens.

Navigate to the location of the lammps out put file for LJ bulk liquid simulation.
|-
|| Select the LJoutput1.atom from the list and click on open button at the bottom-right corner.
|| Select the '''LJoutput1.atom''' from the list and click on''' open '''button at the bottom-right corner.
|-
|| Cursor on the panel.
|| The simulation of the Lennard Jones bulk liqiud opens.

The views from various viewing angles is seen on the panel.
|-
|| Click on the image with the mouse and rotate,
|| Use the mouse to rotate the images on the panel.
|-
|| On the right-side panel click on the '''Particle Types'''
|| On the right-side panel click on the '''Particle Types '''under''' Data Source.'''
|-
|| Particle Types panel opens on the right panel.

In the Appearance section, input the '''Display radius''' as 0.5
|| Particle Types panel opens on the right panel.

In the '''Appearance''' section, input the '''Display radius''' as 0.5 .

This will allow proper rendering of the particles.
|-
|| Cursor on the panel.
|| Will will learn to use more features of '''OVITO''' in the upcoming tutorials.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 6'''

Summary
|| Let's summarize.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment please do the following:

Explore the various various options to change the appearance of the particles.
|-
|| '''Slide Number 8'''
|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Visualizing-the-LAMMPS-Output-using-OVITO/English

2025-07-11T08:24:32Z

Snehalathak:

'''Title of script''': Visualizing the LAMMPS Output using OVITO

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, installation of OVITO, download OVIT, visualize lammps output , video tutorial

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Visualizing the LAMMPS Output using OVITO'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''OVITO''' open visualization tool

Visualize the LAMMPS output file in '''OVITO'''.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

OVITO basic version 3.12.4
|-
|| '''Slide number 4'''

'''Code file'''
|| The following input file is required to practice this tutorial:

LJoutput1.atom

This file is provided in the Code files link of this tutorial page.
|-
|| '''Slide number 5'''

About OVITO

https://www.ovito.org/
|| OVITO is an Open Visualization Tool

It is used for Scientific data visualization and analysis solution for particle-based simulations

OVITO Basic is available free of charge under an open source license.
|-
|| Type ovito.org and press enter.
|| Open any web browser and type ovito.org and press enter.
|-
|| click on the Download button at the center of the page.
|| The web page opens, click on the '''Download''' button at the center of the page.
|-
|| Cursor on the various buttons.

click on Linux button.
|| You will see buttons for downloading installer files for various OS.

User can choose the appropriate button depending on the OS being used.

I will click on Linux button.
|-
|| Cursor on the options.

Click on OVITO basic button.
|| You will see two options, OVITO Basic and OVITOPro.

Click on''' OVITO basic''' button.

The installer files download to you downloads directory.
|-
|| Click on the I'''nstallations Instruction''' link.

Cursor on the
|| Click on the I'''nstallations Instruction''' link given in the middle of the page.

'''Installation''' page opens with detailed information on how to install OVITO on various OS.
|-
|| Open the '''Downloads''' folder and locate the compressed  '''ovito-basic-3.12.4-x86_64.tar.xz'''tar.xz file

Right-click on the file and choose '''Extract Here''' option.
|| Open the '''Downloads''' folder and locate the compressed tar.xz file.

Right-click on the file and choose '''Extract Here''' option.
|-
|| Double-click on the extracted folder.

Double-click on the '''bin '''folder.
|| Double-click on the extracted folder to open it.

Double-click on the '''bin '''folder. The folder opens.
|-
|| Double-click on '''ovito.'''
|| The folder opens, Double-click on '''ovito.'''

'''OVITO''' interface opens.
|-
|| Click on '''File''' menu, from the sub-menu click on '''Load File''' option.
|| Click on '''File''' menu, from the sub-menu click on

'''Load File''' option.
|-
|| Cursor on '''Load File''' pop up box.
|| '''Load File''' pop up box opens.

Navigate to the location of the lammps out put file for LJ bulk liquid simulation.
|-
|| Select the LJoutput1.atom from the list and click on open button at the bottom-right corner.
|| Select the '''LJoutput1.atom''' from the list and click on''' open '''button at the bottom-right corner.
|-
|| Cursor on the panel.
|| The simulation of the Lennard Jones bulk liqiud opens.

The views from various viewing angles is seen on the panel.
|-
|| Click on the image with the mouse anr rotate,
|| Use the mouse to rotate the images on the panel.
|-
|| On the right-side panel click on the '''Particle Types'''
|| On the right-side panel click on the '''Particle Types '''under''' Data Source.'''
|-
|| Particle Types panel opens on the right panel.

In the Appearance section, input the '''Display radius''' as 0.5
|| Particle Types panel opens on the right panel.

In the '''Appearance''' section, input the '''Display radius''' as 0.5 .

This will allow proper rendering of the particles.
|-
|| Cursor on the panel.
|| Will will learn to use more features of '''OVITO''' in the upcoming tutorials.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 6'''

Summary
|| Let's summarize.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment please do the following.

Explore the various various options to change the appearance of the particles.
|-
|| '''Slide Number 8'''
|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Visualizing-the-LAMMPS-Output-using-OVITO/English

2025-07-11T08:23:52Z

Snehalathak: Created page with " '''Title of script''': Visualizing the LAMMPS Output using OVITO '''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi '''Keywords''': LAMMPS, Simulation, installation of OV..."

'''Title of script''': Visualizing the LAMMPS Output using OVITO

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, installation of OVITO, download OVIT, visualize lammps output , video tutorial

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Visualizing the LAMMPS Output using OVITO'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''OVITO''' open visualization tool

Visualize the LAMMPS output file in OVITO.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

OVITO basic version 3.12.4
|-
|| '''Slide number 4'''

'''Code file'''
|| The following input file is required to practice this tutorial:

LJoutput1.atom

This file is provided in the Code files link of this tutorial page.
|-
|| '''Slide number 5'''

About OVITO

https://www.ovito.org/
|| OVITO is an Open Visualization Tool

It is used for Scientific data visualization and analysis solution for particle-based simulations

OVITO Basic is available free of charge under an open source license.
|-
|| Type ovito.org and press enter.
|| Open any web browser and type ovito.org and press enter.
|-
|| click on the Download button at the center of the page.
|| The web page opens, click on the '''Download''' button at the center of the page.
|-
|| Cursor on the various buttons.

click on Linux button.
|| You will see buttons for downloading installer files for various OS.

User can choose the appropriate button depending on the OS being used.

I will click on Linux button.
|-
|| Cursor on the options.

Click on OVITO basic button.
|| You will see two options, OVITO Basic and OVITOPro.

Click on''' OVITO basic''' button.

The installer files download to you downloads directory.
|-
|| Click on the I'''nstallations Instruction''' link.

Cursor on the
|| Click on the I'''nstallations Instruction''' link given in the middle of the page.

'''Installation''' page opens with detailed information on how to install OVITO on various OS.
|-
|| Open the '''Downloads''' folder and locate the compressed  '''ovito-basic-3.12.4-x86_64.tar.xz'''tar.xz file

Right-click on the file and choose '''Extract Here''' option.
|| Open the '''Downloads''' folder and locate the compressed tar.xz file.

Right-click on the file and choose '''Extract Here''' option.
|-
|| Double-click on the extracted folder.

Double-click on the '''bin '''folder.
|| Double-click on the extracted folder to open it.

Double-click on the '''bin '''folder. The folder opens.
|-
|| Double-click on '''ovito.'''
|| The folder opens, Double-click on '''ovito.'''

'''OVITO''' interface opens.
|-
|| Click on '''File''' menu, from the sub-menu click on '''Load File''' option.
|| Click on '''File''' menu, from the sub-menu click on

'''Load File''' option.
|-
|| Cursor on '''Load File''' pop up box.
|| '''Load File''' pop up box opens.

Navigate to the location of the lammps out put file for LJ bulk liquid simulation.
|-
|| Select the LJoutput1.atom from the list and click on open button at the bottom-right corner.
|| Select the '''LJoutput1.atom''' from the list and click on''' open '''button at the bottom-right corner.
|-
|| Cursor on the panel.
|| The simulation of the Lennard Jones bulk liqiud opens.

The views from various viewing angles is seen on the panel.
|-
|| Click on the image with the mouse anr rotate,
|| Use the mouse to rotate the images on the panel.
|-
|| On the right-side panel click on the '''Particle Types'''
|| On the right-side panel click on the '''Particle Types '''under''' Data Source.'''
|-
|| Particle Types panel opens on the right panel.

In the Appearance section, input the '''Display radius''' as 0.5
|| Particle Types panel opens on the right panel.

In the '''Appearance''' section, input the '''Display radius''' as 0.5 .

This will allow proper rendering of the particles.
|-
|| Cursor on the panel.
|| Will will learn to use more features of '''OVITO''' in the upcoming tutorials.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 6'''

Summary
|| Let's summarize.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment please do the following.

Explore the various various options to change the appearance of the particles.
|-
|| '''Slide Number 8'''
|| Thank you
|-
|}

ORCA---Computational-Chemistry/C2/Create-XYZ-File-using-Open-Babel/English

2025-07-09T11:16:54Z

Snehalathak:

'''Title of the script''': Create XYZ File using Open Babel

'''Authors: '''Madhuri Ganapathi, Raj Singh, Snehalatha Kaliappan.

'''Keywords:''' ORCA, Open Babel, Jmol, XYZ file, mol file, SMILES string, orca input file, video tutorial.

{|border=1
|-
|| '''Visual Cue '''
|| '''Narration'''
|-
|| '''Slide Number 1 '''

'''Title slide'''
|| Welcome to this spoken tutorial on '''Create XYZ File using Open Babel'''.
|-
|| '''Slide Number 2 '''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Load water molecule in '''Jmol'''
* Save the file in mol format
* Create SMILES string
* Create XYZ file format using''' Open Babel'''.
|-
|| '''Slide Number 3'''

'''System Requirements'''
|| Here I am using,
* '''Ubuntu Linux '''OS version 22.04
* '''Jmol''' version 16.2.35
* '''Java''' version 11.0.25
* '''Gedit''' text editor version 41.0

A working internet connection.
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''
|| To follow this tutorial, learners should be familiar with the''' Jmol''' interface.

Please watch the Jmol tutorials available on this website.
|-
|| Point to the interface.
|| I have opened the '''Jmol''' interface.
|-
|| Click on File and select '''Get MOL''' option.

In the text box that appears type water and click '''OK''' button.
|| Let us load the water molecule on the Jmol panel.

Click on '''File '''and select '''Get MOL '''option.

In the text box that appears, type water and click '''OK '''button.
|-
|| Point to the water molecule.

Click on the Open model kit icon on the tool bar.

From the options click on minimize.
|| A water molecule appears on the panel.

Click on the '''model kit''' icon.

From the options select '''minimize''' to minimize the structure.
|-
|| Click on Open the model kit.

Select '''save file''' option.

Save dialog box opens.

Type the file name as water.mol and click on Save button.
|| Let us now save the file.

Open the '''model kit''' menu.

Select '''save file''' option.

'''Save''' dialog box opens.

Choose a suitable location to save the file.

Type the file name as '''water.mol''' .

In '''Files of Type''' option select '''Mol.'''

Click on '''Save''' button at the bottom right corner.
|-
|| Cursor on the panel.
|| Let us open the '''2-D Editor '''in '''Jmol'''.
|-
|| Click on '''Tools''' menu, select '''2-D Editor '''from the drop-down
|| Click on''' Tools''' menu, select '''2-D Editor '''from the drop-down.

water molecule is shown in the editor.

Click on the yellow smiley button at the top left of the window.
|-
|| Cursor on the pop-up window.

Copy the '''SMILES''' string(O)for water using Ctrl and C buttons.
|| A small pop-up window opens.

Here we will see capital “'''O'''” which is the '''SMILES''' string for water molecule.

Copy the '''SMILES''' string using Ctrl and C keys.
|-
|| Click on the '''Close''' button on the '''SMILES''' window.
|| Let us close the '''SMILES''' window.
|-
|| '''Slide Number 5'''

'''Create XYZ File Format'''
|| Here we will demonstrate two ways to create XYZ file format using '''Open Babel '''.

One using '''SMILES''' string and the other using a '''mol''' file.

XYZ file format will be used to create input file to run '''ORCA'''.
|-
|| Show Openbabel interface.

[https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html]

point to the page.
|| Open any web browser.

Type '''Openbabel '''in the '''Google''' search bar.

Click on the link '''Open Babel Chemical file format converter.'''

'''Open Babel''' page opens.

This is an online web page to convert chemical structure files to various file formats.
|-
|| Cursor in the open babel page.
|| Let’s demonstrate how to convert a mol file and a '''SMILES '''string to '''xyz''' format.
|-
|| Inside the Input block delete the default SMILE

type the SMILE of water O or '''[OH2]. '''
|| On the left side of the page we can see an '''INPUT''' panel.

In the centre of the page you will see the '''Options''' panel.

On the right side we have an '''OUTPUT '''panel.

In the '''INPUT''' panel delete the default '''SMILE string. '''

Copy'''/'''Paste or type the SMILES string here as '''O''' for water molecule.
|-
|| Point to the''' Options''' window.

Point to the Input format - SMILES.

Select the output format as '''XYZ '''from the drop down list.
|| In the '''Options '''panel, the input format is selected as '''SMILES'''.

Select the output format as '''XYZ '''from the drop down list.
|-
|| In '''Generate Coordinates '''drop down, select''' 3D'''.
|| In the '''Generate Coordinates''' drop down, select''' 3D'''.
|-
|| Click on the “'''Convert” '''button below.

Click on the '''Convert '''button found below the '''Options''' panel.
|| Leave the other options as default.

Click on the '''Convert '''button found below the '''Options''' panel.
|-
|| Navigate to the output section on the right side of the interface.

Click on the download File icon on the top right corner of the Output box.
|| In the '''OUTPUT''' box, '''xyz coordinates''' of the water molecule will appear.

On the top right corner of the ''' Output '''box, click the '''Download File''' icon.
|-
|| In the Save dialog box, In the Name field, the default name '''structure.xyz '''is seen.

Change the name as water.xyz

Click on the Save button at the top right corner of the dialog box.

Show the downloading file.
|| The file downloads as '''structure.xyz''' to my '''Downloads''' folder.

Rename the file as '''water.xyz'''.

If a save file dialog box opens, save the file as '''water.xyz'''.

Back to '''Open Babel Chemical file format converter page'''.
|-
|| Point to the input box.
|| Now let’s convert a mol file to xyz format.

In the '''Open babe'''l page, on the top left side we can see '''Drop or paste here your input file ''' box.
|-
|| Click inside the box, '''File Upload''' window opens.
|| Click inside the box, ''' File Upload''' window opens.
|-
|| Point to the water.mol in the folder.

Select the saved '''water.mol''' file from the folder.

Click the '''Open''' button at the top right corner of the window.
|| Select the saved '''water.mol '''file from the folder.

Click the '''Open''' button at the top right corner of the window.
|-
|| Point to the information.

Point to the word ”string”.

Select the word''' string''' and press '''Delete key '''on the keyboard.
|| The '''INPUT''' box displays the information of the structure.

In the '''INPUT '''box, delete the first line.

The url here.

In some cases you may see a word “string”

This is done to avoid the url or word '''string showing up''' in the output file.
|-
|| From the '''Options '''panel, select the input format as mol--MDL MOL format.
|| From the '''Options''' panel, select the input file format as '''mol--MDL MOL''' format.
|-
|| Select the output format as xyz--XYZ cartesian coordinates format.
|| Now select the output format as xyz-'''XYZ cartesian coordinates format.'''
|-
|| In Generate Coordinates''' '''drop down, select''' 3D'''.
|| In the '''Generate Coordinates''' drop down, select''' 3D'''.
|-
|| Below the '''Options''' box, click on the''' Convert '''button.
|| Leave the other options as such in the panel.

Below the''' Options''' box, click on the '''Convert''' button.
|-
|| Point to the coordinates.

Navigate to the output section on the right side of the interface.
|| In the '''OUTPUT''' box, the xyz coordinates of the water molecule are displayed.
|-
|| Click on the download File icon on the top right corner of the Output box.
|| As explained before, download the xyz file.

Click the '''Download File''' icon in the Output box.

Save the file '''structure.xyz''' as '''water.xyz'''.
|-
|| Right-click on '''water.xyz file.'''

'''Select Open with Text Editor''' option.
|| Let us open the''' Downloads''' folder and navigate to '''water.xyz '''.

Right-click on the file and open the file using a text editor.

Windows users may use notepad or any other text editor.
|-
|| Point to the numbers and xyz coordinates.

Point to the values.
|| The numbers in rows are the '''xyz''' coordinates of the atoms, Oxygen, Hydrogen and Hydrogen.

They are in '''Angstrom '''units.

The values here are tab separated.

We will use this''' water.xyz''' file to create the input file to run '''ORCA.'''
|-
|| '''Slide Number 6'''

'''Summary'''

In this tutorial we have learnt to,

Load water molecule in '''Jmol'''

Save the file in mol format

Create SMILES string

Create XYZ file format using''' Open Babel'''
|| With this we come to the end of this tutorial

Let us summarise.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment
* Generate '''SMILES''' and mol file for carbon monoxide and ammonia molecules using Jmol.
* Create the '''XYZ '''files using '''SMILES''' and mol file in '''Open Babel.'''
|-
|| '''Slide Number 8'''

'''Thank you'''
|| Thank you for joining.
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Simulation-of-Lennard-Jones-Bulk-Liquid/English

2025-07-09T10:34:26Z

Snehalathak:

'''Title of script''': Simulation of Lennard-Jones Bulk Liquid

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, Lennard-Jones bulk liquid, input file, video tutorial

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Simulation of Lennard-Jones Bulk Liquid'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

* Understand the structure of the input script to simulate Lennard-Jones bulk liquid.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Initialize, setup simulation box, create atoms, minimize energy and equilibration.
* Run the simulation.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

Latest stable version of '''LAMMPS''' (LAMMPS Stable Release 29 Aug 2024)

|-
|| '''Slide Number 5'''

'''Prerequisite'''
|| To follow this tutorial learner must be familiar with,

basic computer operations on Linux OS.

|-
|| '''Slide number 6'''

'''Code file'''
|| The following input file is required to practice this tutorial:

LJBulk.txt

This file is provided in the Code files link of this tutorial page.

|-
|| '''Slide Number 7'''

'''LJ Bulk Liquid simulations'''

|| Here are some specific reasons for choosing the '''Lennard-jones''' simulations.

1. Simplicity and Computational Efficiency

2. Benchmarking and Model Testing

3. Risk-Free Exploration of Scenarios

4. Compatibility with Broader Systems

For detailed explanation please refer to the Additional Reading material provided along with this tutorial.

|-
|| Open the input file LJBulk.txt in gedit texttext editor.
|| Running simulations in LAMMPS require an input file.

Download the input file provided along with this tutorial and save it on your system.

Here I have opened the input file in a text editor.

|-
|| Cursor on each section and highlight.
|| The input script is divided into four sections: 

# Initialization
# System definition
# Simulation settings
# Running a simulation

|-
|| Cursor on the input file.
|| Now let us look at what needs to be defined in each section:
|-
|| Cursor on Initialization section.

Line 3: units lj

|| '''Initialization'''

The '''units''' command sets the style of the units for the quantities specified in the input script, data file, and output.

Here we have specified as '''lj'''.

|-
|| Line 4: dimension 3
|| The '''dimension''' command sets the dimension of the simulation.

Here we have 3, since we require the simulation in 3D.

You can set it as 2, if you require a 2D simulation.
|-
|| Line 5: boundary p p p
|| The '''boundary''' command sets the boundary conditions of the simulation box.

here, '''p''' refers periodic.

|-
|| Line 6: atom_style atomic
|| The '''atom_style''' command defines necessary per-atom attributes for simulation models and data handling.

|-
|| Cursor on System definition section.

Line 12: region box block 0 20 0 20 0 20 units box

region liquid block 1 19 1 19 1 10

create_atoms1 random 1754 12345 liquid

mass 1 1.0
|| '''System definition:'''

Here we define a geometric region of space in x, y and z direction.

We specified number 20 here.

This number can be small or big, depending on the requirement of the simulation box.

|-
|| Line 13: It is on line 14create_box 1 box
|| Defining simulation box

Here 1 indicates the number of atom types present in the system.

For example, if the system consists of 3 types of particles, then 1 should be replaced with 3 and so on.

|-
|| Line 16: region liquid block 1 19 1 19 1 10
|| Defining a geometric region to place the liquid atoms.

Here, liquid is a group ID.

The numbers are positioned low and high in X, Y and Z directions.

We have defined 1 as low and 19 as high.

Based on this number we have to calculate the number of type 1 atoms as defined in the next line.

|-
|| Line 17: create_atoms1 random 1926 12345 liquid
|| Creation of liquid atoms in the defined region “liquid”. 

Example: ''create_atoms'' 1 ''random'' 1926 12345 liquid

Here, 1926 is the number of type 1 atoms.

Please see the Additional Reading material for details of calculating this number.

12345 is the random number to put the type 1 particles randomly in the defined region '''liquid'''.

|-
|| Line 18:It is on line 19 mass 1 1.0
|| Defining the mass of the particle.

Here, 1 and 1.0 represents type “1” particle and mass of the particle respectively.

|-
|| Line 24: pair_style lj/cut 2.5
|| Next in '''Simulation Settings:'''

cutoff calculates the pairwise distances within the mentioned cutoff.

|-
|| Line 30: group liq type 1
|| Here we enter the numbers that describe how atom pairs interact.

Here, all type 1 particles are grouped with a group ID '''liq'''.

|-
|| Line 34: minimize 1e-6 1e-6 10000 10000
|| '''Running a simulation:'''

Minimization of the system to remove the overlap between the particles.

These numbers indicate tolerance, force tolerance, max iteration, max evaluations.

|-
|| Line 38: neighbor 0.3 bin

Line 39: neigh_modify every 1 delay 0 check yes page 100000 one 5000
|| Building of pairwise neighbor lists.

This command sets parameters that affect the building of pairwise neighbor lists.

|-
|| Line 44: dump 1 liq atom 5 output.atom
|| Storing the position of all the coordinates to the file.

Here 5 is the frequency of printing the output file and in the end gives the name for the output file.

Here we are naming it '''output.atom'''.

|-
|| Line 46: thermo_style custom step etotal
|| Logging the desired data during the simulation.

''Here, other parameters can also be printed, and will be discussed in the upcoming tutorials.''

|-
|| Line 48: timestep 0.005

Line 49: thermo 5
|| The '''timestep''' command sets the timestep size for the simulation.

The '''thermo '''command computes and prints the desired thermodynamic information like:

temperature, energy, pressure at the mentioned interval of time.

Number 5 here indicates the frequency of printing output.
|-
|| Line 53: fix 1 liq npt temp 0.8 0.8 100 iso 1 1 100
|| In LAMMPS, a''' fix''' is any operation that is applied to the system during timestepping or minimization

The '''npt''' command performs the time integration using equations of motion to generate positions and velocities for atoms.

In an '''npt''' ensemble:

the number of particles, pressure of the system and temperature of the system are held constant.

|-
|| Line 55: run 10
|| Here 10 indicates timesteps_number.

The large number will make the simulation more clear to visualize.

The time taken to complete the simulation will also increase.

For the sake of simplicity we have indicated 10 timesteps

|-
|| Cursor on the input file.

Close the text editor.
|| Now let me demonstrate how to run this input file.

Close the text editor.

|-
|| Go to the folder where input file is located.

Open the folder and show the input file.
|| I have saved the input file in a folder in my home directory.

Navigate to the input file location.
|-
|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|| As LAMMPS is already installed in your computer.

Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|-
|| Cursor on the terminal.
|| Alternatively you can open the terminal and navigate to the path leading to the input file.
|-
|| At the prompt type “ '''lmp_serial -in Ljbulk.txt'''”

Press Enter.
|| Type the following command at the prompt to run the input file.

'''lmp_serial -in LJbulk.txt'''

Windows users can open the command prompt, type the command and proceed as shown.

Press Enter.
|-
|| Cursor on the terminal.

Open the folder containing the input file to show '''log.lammps''' and '''output.atom.'''
|| The output is seen on the terminal.

Two output files are generated, '''log.lammps''' and '''output.atom. '''

These files will be saved in the same folder where your input file is located.

|-
|| Cursor on the folder.
|| The analysis and visualization of the output file will be covered in the upcoming tutorial.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary '''
|| Let's summarize.

|-
|| '''Slide Number 9'''

'''Assignment'''

Edit the line in the System Definition section as follows

''region liquid block 1 25 1 25 1 15''

|| As an assignment,

Edit the line in the System Definition section as follows:

Calculate the number of atoms and replace the number in the subsequent line.

Save and run the input file.

|-
|| '''Slide Number 10'''

Thank you

|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Simulation-of-Lennard-Jones-Bulk-Liquid/English

2025-07-09T10:31:00Z

Snehalathak:

'''Title of script''': Simulation of Lennard-Jones Bulk Liquid

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, Lennard-Jones bulk liquid, input file, video tutorial

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Simulation of Lennard-Jones Bulk Liquid'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

* Understand the structure of the input script to simulate Lennard-Jones bulk liquid.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Initialize, setup simulation box, create atoms, minimize energy and equilibration.
* Run the simulation.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

Latest stable version of '''LAMMPS''' (LAMMPS Stable Release 29 Aug 2024)

|-
|| '''Slide Number 5'''

'''Prerequisite'''
|| To follow this tutorial learner must be familiar with,

basic computer operations on Linux OS.

|-
|| '''Slide number 6'''

'''Code file'''
|| The following input file is required to practice this tutorial:

LJBulk.txt

This file is provided in the Code files link of this tutorial page.

|-
|| '''Slide Number 7'''

'''LJ Bulk Liquid simulations'''

|| Here are some specific reasons for choosing the '''Lennard-jones''' simulations.

1. Simplicity and Computational Efficiency

2. Benchmarking and Model Testing

3. Risk-Free Exploration of Scenarios

4. Compatibility with Broader Systems

For detailed explanation please refer to the Additional Reading material provided along with this tutorial.

|-
|| Open the input file LJBulk.txt in gedit texttext editor.
|| Running simulations in LAMMPS require an input file.

Download the input file provided along with this tutorial and save it on your system.

Here I have opened the input file in a text editor.

|-
|| Cursor on each section and highlight.
|| The input script is divided into four sections: 

# Initialization
# System definition
# Simulation settings
# Running a simulation

|-
|| Cursor on the input file.
|| Now let us look at what needs to be defined in each section:
|-
|| Cursor on Initialization section.

Line 3: units lj

|| '''Initialization'''

The '''units''' command sets the style of the units for the quantities specified in the input script, data file, and output.

Here we have specified as '''lj'''.

|-
|| Line 4: dimension 3
|| The '''dimension''' command sets the dimension of the simulation.

Here we have 3, since we require the simulation in 3D.

You can set it as 2, if you require a 2D simulation.
|-
|| Line 5: boundary p p p
|| The '''boundary''' command sets the boundary conditions of the simulation box.

here, '''p''' refers periodic

|-
|| Line 6: atom_style atomic
|| The '''atom_style''' command defines necessary per-atom attributes for simulation models and data handling.

|-
|| Cursor on System definition section.

Line 12: region box block 0 20 0 20 0 20 units box

region liquid block 1 19 1 19 1 10

create_atoms1 random 1754 12345 liquid

mass 1 1.0
|| '''System definition:'''

Here we define a geometric region of space in x, y and z direction.

We specified number 20 here.

This number can be small or big, depending on the requirement of the simulation box.

|-
|| Line 13: It is on line 14create_box 1 box
|| Defining simulation box

Here 1 indicates the number of atom types present in the system.

For example, if the system consists of 3 types of particles, then 1 should be replaced with 3 and so on.

|-
|| Line 16: region liquid block 1 19 1 19 1 10
|| Defining a geometric region to place the liquid atoms.

Here, liquid is a group ID.

The numbers are positioned low and high in X, Y and Z directions.

We have defined 1 as low and 19 as high.

Based on this number we have to calculate the number of type 1 atoms as defined in the next line.

|-
|| Line 17: create_atoms1 random 1926 12345 liquid
|| Creation of liquid atoms in the defined region “liquid”. 

Example: ''create_atoms'' 1 ''random'' 1926 12345 liquid

Here, 1926 is the number of type 1 atoms.

Please see the Additional Reading material for details of calculating this number.

12345 is the random number to put the type 1 particles randomly in the defined region '''liquid'''.

|-
|| Line 18:It is on line 19 mass 1 1.0
|| Defining the mass of the particle.

Here, 1 and 1.0 represents type “1” particle and mass of the particle respectively.

|-
|| Line 24: pair_style lj/cut 2.5
|| Next in '''Simulation Settings:'''

cutoff calculates the pairwise distances within the mentioned cutoff.

|-
|| Line 30: group liq type 1
|| Here we enter the numbers that describe how atom pairs interact.

Here, all type 1 particles are grouped with a group ID '''liq'''.

|-
|| Line 34: minimize 1e-6 1e-6 10000 10000
|| '''Running a simulation:'''

Minimization of the system to remove the overlap between the particles.

These numbers indicate tolerance, force tolerance, max iteration, max evaluations.

|-
|| Line 38: neighbor 0.3 bin

Line 39: neigh_modify every 1 delay 0 check yes page 100000 one 5000
|| Building of pairwise neighbor lists.

This command sets parameters that affect the building of pairwise neighbor lists.

|-
|| Line 44: dump 1 liq atom 5 output.atom
|| Storing the position of all the coordinates to the file.

Here 5 is the frequency of printing the output file and in the end gives the name for the output file.

Here we are naming it '''output.atom'''.

|-
|| Line 46: thermo_style custom step etotal
|| Logging the desired data during the simulation.

''Here, other parameters can also be printed, and will be discussed in the upcoming tutorials.''

|-
|| Line 48: timestep 0.005

Line 49: thermo 5
|| The '''timestep''' command sets the timestep size for the simulation.

The '''thermo '''command computes and prints the desired thermodynamic information like:

temperature, energy, pressure at the mentioned interval of time.

Number 5 here indicates the frequency of printing output.
|-
|| Line 53: fix 1 liq npt temp 0.8 0.8 100 iso 1 1 100
|| In LAMMPS, a''' fix''' is any operation that is applied to the system during timestepping or minimization

The '''npt''' command performs the time integration using equations of motion to generate positions and velocities for atoms.

In an '''npt''' ensemble:

the number of particles, pressure of the system and temperature of the system are held constant.

|-
|| Line 55: run 10
|| Here 10 indicates timesteps_number.

The large number will make the simulation more clear to visualize.

The time taken to complete the simulation will also increase.

For the sake of simplicity we have indicated 10 timesteps

|-
|| Cursor on the input file.

Close the text editor.
|| Now let me demonstrate how to run this input file.

Close the text editor.

|-
|| Go to the folder where input file is located.

Open the folder and show the input file.
|| I have saved the input file in a folder in my home directory.

Navigate to the input file location.
|-
|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|| As LAMMPS is already installed in your computer.

Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|-
|| Cursor on the terminal.
|| Alternatively you can open the terminal and navigate to the path leading to the input file.
|-
|| At the prompt type “ '''lmp_serial -in Ljbulk.txt'''”

Press Enter.
|| Type the following command at the prompt to run the input file.

'''lmp_serial -in LJbulk.txt'''

Windows users can open the command prompt, type the command and proceed as shown.

Press Enter.
|-
|| Cursor on the terminal.

Open the folder containing the input file to show '''log.lammps''' and '''output.atom.'''
|| The output is seen on the terminal.

Two output files are generated, '''log.lammps''' and '''output.atom. '''

These files will be saved in the same folder where your input file is located.

|-
|| Cursor on the folder.
|| The analysis and visualization of the output file will be covered in the upcoming tutorial.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary '''
|| Let's summarize.

|-
|| '''Slide Number 9'''

'''Assignment'''

Edit the line in the System Definition section as follows

''region liquid block 1 25 1 25 1 15''

|| As an assignment,

Edit the line in the System Definition section as follows:

Calculate the number of atoms and replace the number in the subsequent line.

Save and run the input file.

|-
|| '''Slide Number 10'''

Thank you

|| Thank you
|-
|}

ORCA---Computational-Chemistry/C2/Create-XYZ-File-using-Open-Babel/English

2025-07-09T09:22:43Z

Snehalathak: Created page with " '''Title of the script''': Create XYZ File using Open Babel '''Author: '''Madhuri Ganapathi, Raj Singh '''Keywords:''' ORCA, Open Babel, Jmol, XYZ file, mol file, SMILES s..."

'''Title of the script''': Create XYZ File using Open Babel

'''Author: '''Madhuri Ganapathi, Raj Singh

'''Keywords:''' ORCA, Open Babel, Jmol, XYZ file, mol file, SMILES string, orca input file, video tutorial.

{|border=1
|-
|| '''Visual Cue '''
|| '''Narration'''
|-
|| '''Slide Number 1 '''

'''Title slide'''
|| Welcome to this spoken tutorial on '''Create XYZ File using Open Babel'''.
|-
|| '''Slide Number 2 '''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Load water molecule in '''Jmol'''
* Save the file in mol format
* Create SMILES string
* Create XYZ file format using''' Open Babel'''
|-
|| '''Slide Number 3'''

'''System Requirements'''
|| Here I am using,
* '''Ubuntu Linux '''OS version 22.04
* Jmol version 16.2.35
* Java version 11.0.25
* Gedit text editor version 41.0

A working internet connection
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''
|| To follow this tutorial, learners should be familiar with the''' Jmol''' interface

Please watch the Jmol tutorials available on this website
|-
|| Point to the interface.
|| I have opened the Jmol interface.
|-
|| Click on File and select Get MOL option.

In the text box that appears type water and click OK button
|| Let us load the water molecule on the Jmol panel.

Click on '''File '''and select '''Get MOL '''option.

In the text box that appears, type water and click '''OK '''button.
|-
|| Point to the water molecule.

Click on the Open model kit icon on the tool bar.

From the options click on minimize.
|| A water molecule appears on the panel.

Click on the model kit icon.

From the options select '''minimize''' to minimize the structure.
|-
|| Click on Open the model kit.

Select '''save file''' option.

Save dialog box opens.

Type the file name as water.mol and click on Save button.
|| Let us now save the file.

Open the model kit menu.

Select '''save file''' option.

Save dialog box opens.

Choose a suitable location to save the file.

Type the file name as '''water.mol''' .

In Files of type option select '''Mol.'''

Click on '''Save''' button at the bottom right corner.
|-
|| Cursor on the panel.
|| Let us open the '''2-D Editor '''in '''Jmol'''.
|-
|| Click on '''Tools''' menu, select '''2-D Editor '''from the drop-down
|| Click on''' Tools''' menu, select '''2-D Editor '''from the drop-down.

water molecule is shown in the editor.

Click on the yellow smiley button at the top left of the window.
|-
|| Cursor on the pop-up window.

Copy the '''SMILES''' string(O)for water using Ctrl and C buttons.
|| A small pop-up window opens.

Here we will see capital “'''O'''” which is the SMILES string for water molecule.

Copy the '''SMILES''' string using Ctrl and C keys.
|-
|| Click on the '''Close''' button on the '''SMILES''' window.
|| Let us close the '''SMILES''' window.
|-
|| '''Slide Number 5'''

'''Create XYZ File Format'''
|| Here we will demonstrate two ways to create XYZ file format using '''Open Babel '''

One using SMILES string and the other using a mol file.

XYZ file format will be used to create input file to run ORCA.
|-
|| Show Openbabel interface.

[https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html]

point to the page.
|| Open any web browser.

Type '''Openbabel '''in the Google search bar.

Click on the link '''Open Babel Chemical file format converter.'''

'''Open Babel''' page opens.

This is an online web page to convert chemical structure files to various file formats.
|-
|| Cursor in the open babel page.
|| Let’s demonstrate how to convert a mol file and a '''SMILES '''string to '''xyz''' format.
|-
|| Inside the Input block delete the default SMILE

type the SMILE of water O or '''[OH2]. '''
|| On the left side of the page we can see an '''INPUT''' panel.

In the centre of the page you will see the '''Options''' panel.

On the right side we have an '''OUTPUT '''panel.

In the Input panel delete the default '''SMILE string. '''

Copy'''/'''Paste or type the SMILES string here as '''O''' for water molecule.
|-
|| Point to the''' Options''' window.

Point to the Input format - SMILES.

Select the output format as '''XYZ '''from the drop down list.
|| In the '''Options '''panel, the input format is selected as '''SMILES'''.

Select the output format as '''XYZ '''from the drop down list.
|-
|| In '''Generate Coordinates '''drop down, select''' 3D'''.
|| In the '''Generate Coordinates''' drop down, select''' 3D'''.
|-
|| Click on the “'''Convert” '''button below.

Click on the '''Convert '''button found below the '''Options''' panel.
|| Leave the other options as default.

Click on the '''Convert '''button found below the '''Options''' panel.
|-
|| Navigate to the output section on the right side of the interface.

Click on the download File icon on the top right corner of the Output box.
|| In the '''OUTPUT''' box, '''xyz coordinates''' of the water molecule will appear.

On the top right corner of the''' Output '''box, click the '''Download File''' icon.
|-
|| In the Save dialog box, In the Name field, the default name '''structure.xyz '''is seen.

Change the name as water.xyz

Click on the Save button at the top right corner of the dialog box.

Show the downloading file.
|| The file downloads as '''structure.xyz''' to my downloads folder.

Rename the file as''' [http://water.xyz/ water.xyz].'''

If a save file dialog box opens, save the file as '''water.xyz'''.

Back to '''Open Babel Chemical file format converter page.'''
|-
|| Point to the input box.
|| Now let’s convert a mol file to xyz format.

In the Open babel page, on the top left side we can see '''Drop or paste here your input file '''box.
|-
|| Click inside the box, '''File Upload''' window opens.
|| Click inside the box,''' File Upload''' window opens.
|-
|| Point to the water.mol in the folder.

Select the saved water.mol file from the folder.

Click the Open button at the top right corner of the window.
|| Select the saved '''water.mol '''file from the folder.

Click the '''Open''' button at the top right corner of the window.
|-
|| Point to the information.

Point to the word ”string”.

Select the word''' string''' and press '''Delete key '''on the keyboard.
|| The '''INPUT''' box displays the information of the structure.

In the '''INPUT '''box, delete the first line.

The url here.

In some cases you may see a word “string”

This is done to avoid the url or word '''string showing up''' in the output file.
|-
|| From the '''Options '''panel, select the input format as mol--MDL MOL format.
|| From the '''Options''' panel, select the input file format as '''mol--MDL MOL''' format.
|-
|| Select the output format as xyz--XYZ cartesian coordinates format.
|| Now select the output format as xyz-'''XYZ cartesian coordinates format.'''
|-
|| In Generate Coordinates''' '''drop down, select''' 3D'''.
|| In the '''Generate Coordinates''' drop down, select''' 3D'''.
|-
|| Below the '''Options''' box, click on the''' Convert '''button.
|| Leave the other options as such in the panel.

Below the''' Options''' box, click on the '''Convert''' button.
|-
|| Point to the coordinates.

Navigate to the output section on the right side of the interface.
|| In the '''OUTPUT''' box, the xyz coordinates of the water molecule are displayed.
|-
|| Click on the download File icon on the top right corner of the Output box.
|| As explained before, download the xyz file. Click the '''Download File''' icon in the Output box.

Save the file '''structure.xyz''' as '''water.xyz'''.
|-
|| Right-click on '''water.xyz file.'''

'''Select Open with Text Editor''' option.
|| Let us open the''' Downloads''' folder and navigate to '''water.xyz .'''

Right-click on the file and open the file using a text editor.

Windows users may use notepad or any other text editor.
|-
|| Point to the numbers and xyz coordinates.

Point to the values.
|| The numbers in rows are the '''xyz''' coordinates of the atoms, Oxygen, Hydrogen and Hydrogen.

They are in '''Angstrom '''units.

The values here are tab separated.

We will use this''' water.xyz''' file to create the input file to run '''ORCA.'''
|-
|| '''Slide Number 6'''

'''Summary'''

In this tutorial we have learnt to,

Load water molecule in '''Jmol'''

Save the file in mol format

Create SMILES string

Create XYZ file format using''' Open Babel'''
|| With this we come to the end of this tutorial

Let us summarise.
|-
|| '''Slide Number 7'''

'''Assignment'''
|| As an assignment
* Generate '''SMILES''' and mol file for carbon monoxide and ammonia molecules using Jmol.
* Create the '''XYZ '''files using '''SMILES''' and mol file in '''Open Babel.'''
|-
|| '''Slide Number 8'''

'''Thank you'''
|| Thank you for joining.
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Simulation-of-Lennard-Jones-Bulk-Liquid/English

2025-07-09T06:15:24Z

Snehalathak:

'''Title of script''': Simulation of Lennard-Jones Bulk Liquid

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, Lennard-Jones bulk liquid, input file, video tutorial

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Simulation of Lennard-Jones Bulk Liquid'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

* Understand the structure of the input script to simulate Lennard-Jones bulk liquid.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Initialize, setup simulation box, create atoms, minimize energy and equilibration.
* Run the simulation.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

Latest stable version of '''LAMMPS''' (LAMMPS Stable Release 29 Aug 2024)

|-
|| '''Slide Number 5'''

'''Prerequisite'''
|| To follow this tutorial learner must be familiar with,

basic computer operations on Linux OS.

|-
|| '''Slide number 6'''

'''Code file'''
|| The following input file is required to practice this tutorial:

LJBulk.txt

This file is provided in the Code files link of this tutorial page.

|-
|| '''Slide Number 7'''

'''LJ Bulk Liquid simulations'''

|| Here are some specific reasons for choosing the '''Lennard-jones''' simulations.

Simplicity and Computational Efficiency

Benchmarking and Model Testing

Risk-Free Exploration of Scenarios

Compatibility with Broader Systems

For detailed explanation please refer to the Additional Reading material provided along with this tutorial.

|-
|| Open the input file LJBulk.txt in gedit texttext editor.
|| Running simulations in LAMMPS require an input file.

Download the input file provided along with this tutorial and save it on your system.

Here I have opened the input file in a text editor.

|-
|| Cursor on each section and highlight.
|| The input script is divided into four sections: 

# Initialization
# System definition
# Simulation settings
# Running a simulation

|-
|| Cursor on the input file.
|| Now let us look at what needs to be defined in each section:
|-
|| Cursor on Initialization section.

Line 3: units lj

|| '''Initialization'''

The '''units''' command sets the style of the units for the quantities specified in the input script, data file, and output.

Here we have specified as lj.

|-
|| Line 4: dimension 3
|| The '''dimension''' command sets the dimension of the simulation.

Here we have 3, since we require the simulation in 3D.

You can set it as 2, if you require a 2D simulation.
|-
|| Line 5: boundary p p p
|| The '''boundary''' command sets the boundary conditions of the simulation box.

here, '''p''' refers periodic

|-
|| Line 6: atom_style atomic
|| The '''atom_style''' command defines necessary per-atom attributes for simulation models and data handling.

|-
|| Cursor on System definition section.

Line 12: region box block 0 20 0 20 0 20 units box

region liquid block 1 19 1 19 1 10

create_atoms1 random 1754 12345 liquid

mass 1 1.0
|| '''System definition:'''

Here we define a geometric region of space in x, y and z direction.

We specified number 20 here.

This number can be small or big, depending on the requirement of the simulation box.

|-
|| Line 13: It is on line 14create_box 1 box
|| Defining simulation box

Here '''1''' indicates the number of atom types present in the system.

For example, if the system consists of '''3 '''types of particles, then '''1''' should be replaced with '''3 ''' and so on.

|-
|| Line 16: region liquid block 1 19 1 19 1 10
|| Defining a geometric region to place the liquid atoms.

Here, liquid is a group ID, the numbers are positioned low and high in X, Y and Z directions.

We have defined 1 as low and 19 as high.

Based on this number we have to calculate the number of type 1 atoms as defined in the next line.

|-
|| Line 17: create_atoms1 random 1926 12345 liquid
|| Creation of liquid atoms in the defined region “liquid”. 

Example: ''create_atoms'' 1 ''random'' 1926 12345 liquid

Here, 1926 is the number of type 1 atoms.

Please see the Additional Reading material for details of calculating this number.

12345 is the random number to put the type 1 particles randomly in the defined region '''liquid'''.

|-
|| Line 18:It is on line 19 mass 1 1.0
|| Defining the mass of the particle.

Here, 1 and 1.0 represents type “1” particle and mass of the particle respectively

|-
|| Line 24: pair_style lj/cut 2.5
|| Next in '''Simulation Settings:'''

cutoff calculates the pairwise distances within the mentioned cutoff.

|-
|| Line 30: group liq type 1
|| Here we enter the numbers that describe how atom pairs interact.

Here, all type 1 particles are grouped with a group ID liq.

|-
|| Line 34: minimize 1e-6 1e-6 10000 10000
|| '''Running a simulation:'''

Minimization of the system to remove the overlap between the particles.

These numbers indicate tolerance, force tolerance, max iteration, max evaluations.

|-
|| Line 38: neighbor 0.3 bin

Line 39: neigh_modify every 1 delay 0 check yes page 100000 one 5000
|| Building of pairwise neighbor lists.

This command sets parameters that affect the building of pairwise neighbor lists.

|-
|| Line 44: dump 1 liq atom 5 output.atom
|| Storing the position of all the coordinates to the file.

Here 5 is the frequency of printing the output file and in the end gives the name for the output file.

Here we are naming it output.atom.

|-
|| Line 46: thermo_style custom step etotal
|| Logging the desired data during the simulation.

''Here, other parameters can also be printed, and will be discussed in the upcoming tutorials.''

|-
|| Line 48: timestep 0.005

Line 49: thermo 5
|| The '''timestep''' command sets the timestep size for the simulation.

The '''thermo '''command computes and prints the desired thermodynamic information like:

temperature, energy, pressure at the mentioned interval of time.

Number 5 here indicates the frequency of printing output.
|-
|| Line 53: fix 1 liq npt temp 0.8 0.8 100 iso 1 1 100
|| In LAMMPS, a''' fix''' is any operation that is applied to the system during timestepping or minimization

The '''npt''' command performs the time integration''' '''using equations of motion to generate positions and velocities for atoms.

In an '''np'''t ensemble:

the number of particles, pressure of the system and temperature of the system are held constant.

|-
|| Line 55: run 10
|| Here 10 indicates timesteps_number.

The large number will make the simulation more clear to visualize .

The time taken to complete the simulation will also increase.

For the sake of simplicity we have indicated 10 timesteps

|-
|| Cursor on the input file.

Close the text editor.
|| Now let me demonstrate how to run this input file.

Close the text editor.

|-
|| Go to the folder where input file is located.

Open the folder and show the input file.
|| I have saved the input file in a folder in my home directory.

Navigate to the input file location.
|-
|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|| As LAMMPS is already installed in your computer.

Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|-
|| Cursor on the terminal.
|| Alternatively you can open the terminal and navigate to the path leading to the input file.
|-
|| At the prompt type “ '''lmp_serial -in Ljbulk.txt'''”

Press enter
|| Type the following command at the prompt to run the input file.

'''lmp_serial -in LJbulk.txt'''

Windows users can open the command prompt, type the command and proceed as shown.

Press enter
|-
|| Cursor on the terminal.

Open the folder containing the input file to show '''log.lammps''' and '''output.atom..'''
|| The output is seen on the terminal.

Two output files are generated, '''log.lammps''' and '''output.atom. '''

These files will be saved in the same folder where your input file is located.

|-
|| Cursor on the folder.
|| The analysis and visualization of the output file will be covered in the upcoming tutorial.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary '''
|| Let's summarize.

|-
|| '''Slide Number 9'''

'''Assignment'''

Edit the line in the System Definition section as follows

''region liquid block 1 25 1 25 1 15''

|| As an assignment,

Edit the line in the System Definition section as follows

Calculate the number of atoms and replace the number in the subsequent line.

Save and run the input file.

|-
|| '''Slide Number 10'''

Thank you

|| Thank you
|-
|}

LAMMPS-Molecular-Dynamics-Simulator/C2/Simulation-of-Lennard-Jones-Bulk-Liquid/English

2025-07-09T06:15:05Z

Snehalathak: Created page with " '''Title of script''': Simulation of Lennard-Jones Bulk Liquid '''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi '''Keywords''': LAMMPS, Simulation, Lennard-Jones bulk..."

'''Title of script''': Simulation of Lennard-Jones Bulk Liquid

'''Author: '''Dr.Snehalatha Kaliappan, Prasad Baddi

'''Keywords''': LAMMPS, Simulation, Lennard-Jones bulk liquid, input file, video tutorial

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Simulation of Lennard-Jones Bulk Liquid'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

* Understand the structure of the input script to simulate Lennard-Jones bulk liquid.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

* Initialize, setup simulation box, create atoms, minimize energy and equilibration.
* Run the simulation.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| To record this tutorial, I am using,

'''Ubuntu Linux '''OS version 22.04

Latest stable version of '''LAMMPS''' (LAMMPS Stable Release 29 Aug 2024)

|-
|| '''Slide Number 5'''

'''Prerequisite'''
|| To follow this tutorial learner must be familiar with,

basic computer operations on Linux OS.

|-
|| '''Slide number 6'''

'''Code file'''
|| The following input file is required to practice this tutorial:

LJBulk.txt

This file is provided in the Code files link of this tutorial page.

|-
|| '''Slide Number 7'''

'''LJ Bulk Liquid simulations'''

|| Here are some specific reasons for choosing the '''Lennard-jones''' simulations.

Simplicity and Computational Efficiency

Benchmarking and Model Testing

Risk-Free Exploration of Scenarios

Compatibility with Broader Systems

For detailed explanation please refer to the Additional Reading material provided along with this tutorial.

|-
|| Open the input file LJBulk.txt in gedit texttext editor.
|| Running simulations in LAMMPS require an input file.

Download the input file provided along with this tutorial and save it on your system.

Here I have opened the input file in a text editor.

|-
|| Cursor on each section and highlight.
|| The input script is divided into four sections: 

# Initialization
# System definition
# Simulation settings
# Running a simulation

|-
|| Cursor on the input file.
|| Now let us look at what needs to be defined in each section:
|-
|| Cursor on Initialization section.

Line 3: units lj

|| '''Initialization'''

The '''units''' command sets the style of the units for the quantities specified in the input script, data file, and output.

Here we have specified as lj.

|-
|| Line 4: dimension 3
|| The '''dimension''' command sets the dimension of the simulation.

Here we have 3, since we require the simulation in 3D.

You can set it as 2, if you require a 2D simulation.
|-
|| Line 5: boundary p p p
|| The '''boundary''' command sets the boundary conditions of the simulation box.

here, '''p''' refers periodic

|-
|| Line 6: atom_style atomic
|| The '''atom_style''' command defines necessary per-atom attributes for simulation models and data handling.

|-
|| Cursor on System definition section.

Line 12: region box block 0 20 0 20 0 20 units box

region liquid block 1 19 1 19 1 10

create_atoms1 random 1754 12345 liquid

mass 1 1.0
|| '''System definition:'''

Here we define a geometric region of space in x, y and z direction.

We specified number 20 here.

This number can be small or big, depending on the requirement of the simulation box.

|-
|| Line 13: It is on line 14create_box 1 box
|| Defining simulation box

Here '''1''' indicates the number of atom types present in the system.

For example, if the system consists of '''3 '''types of particles, then '''1''' should be replaced with '''3 ''' and so on.

|-
|| Line 16: region liquid block 1 19 1 19 1 10
|| Defining a geometric region to place the liquid atoms.

Here, liquid is a group ID, the numbers are positioned low and high in X, Y and Z directions.

We have defined 1 as low and 19 as high.

Based on this number we have to calculate the number of type 1 atoms as defined in the next line.

|-
|| Line 17: create_atoms1 random 1926 12345 liquid
|| Creation of liquid atoms in the defined region “liquid”. 

Example: ''create_atoms'' 1 ''random'' 1926 12345 liquid

Here, 1926 is the number of type 1 atoms.

Please see the Additional Reading material for details of calculating this number.

12345 is the random number to put the type 1 particles randomly in the defined region '''liquid'''.

|-
|| Line 18:It is on line 19 mass 1 1.0
|| Defining the mass of the particle.

Here, 1 and 1.0 represents type “1” particle and mass of the particle respectively

|-
|| Line 24: pair_style lj/cut 2.5
|| Next in '''Simulation Settings:'''

cutoff calculates the pairwise distances within the mentioned cutoff.

|-
|| Line 30: group liq type 1
|| Here we enter the numbers that describe how atom pairs interact.

Here, all type 1 particles are grouped with a group ID liq.

|-
|| Line 34: minimize 1e-6 1e-6 10000 10000
|| '''Running a simulation:'''

Minimization of the system to remove the overlap between the particles.

These numbers indicate tolerance, force tolerance, max iteration, max evaluations.

|-
|| Line 38: neighbor 0.3 bin

Line 39: neigh_modify every 1 delay 0 check yes page 100000 one 5000
|| Building of pairwise neighbor lists.

This command sets parameters that affect the building of pairwise neighbor lists.

|-
|| Line 44: dump 1 liq atom 5 output.atom
|| Storing the position of all the coordinates to the file.

Here 5 is the frequency of printing the output file and in the end gives the name for the output file.

Here we are naming it output.atom.

|-
|| Line 46: thermo_style custom step etotal
|| Logging the desired data during the simulation.

''Here, other parameters can also be printed, and will be discussed in the upcoming tutorials.''

|-
|| Line 48: timestep 0.005

Line 49: thermo 5
|| The '''timestep''' command sets the timestep size for the simulation.

The '''thermo '''command computes and prints the desired thermodynamic information like:

temperature, energy, pressure at the mentioned interval of time.

Number 5 here indicates the frequency of printing output.
|-
|| Line 53: fix 1 liq npt temp 0.8 0.8 100 iso 1 1 100
|| In LAMMPS, a''' fix''' is any operation that is applied to the system during timestepping or minimization

The '''npt''' command performs the time integration''' '''using equations of motion to generate positions and velocities for atoms.

In an '''np'''t ensemble:

the number of particles, pressure of the system and temperature of the system are held constant.

|-
|| Line 55: run 10
|| Here 10 indicates timesteps_number.

The large number will make the simulation more clear to visualize .

The time taken to complete the simulation will also increase.

For the sake of simplicity we have indicated 10 timesteps

|-
|| Cursor on the input file.

Close the text editor.
|| Now let me demonstrate how to run this input file.

Close the text editor.

|-
|| Go to the folder where input file is located.

Open the folder and show the input file.
|| I have saved the input file in a folder in my home directory.

Navigate to the input file location.
|-
|| Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|| As LAMMPS is already installed in your computer.

Right click on the folder containing the input file.

From the context menu choose '''Open in Terminal '''option.
|-
|| Cursor on the terminal.
|| Alternatively you can open the terminal and navigate to the path leading to the input file.
|-
|| At the prompt type “ '''lmp_serial -in Ljbulk.txt'''”

Press enter
|| Type the following command at the prompt to run the input file.

'''lmp_serial -in LJbulk.txt'''

Windows users can open the command prompt, type the command and proceed as shown.

Press enter
|-
|| Cursor on the terminal.

Open the folder containing the input file to show '''log.lammps''' and '''output.atom..'''
|| The output is seen on the terminal.

Two output files are generated, '''log.lammps''' and '''output.atom. '''

These files will be saved in the same folder where your input file is located.

|-
|| Cursor on the folder.
|| The analysis and visualization of the output file will be covered in the upcoming tutorial.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary '''
|| Let's summarize.

|-
|| '''Slide Number 9'''

'''Assignment'''

Edit the line in the System Definition section as follows

''region liquid block 1 25 1 25 1 15''

|| As an assignment,

Edit the line in the System Definition section as follows

Calculate the number of atoms and replace the number in the subsequent line.

Save and run the input file.

|-
|| '''Slide Number 10'''

Thank you

|| Thank you
|-
|}

Process-Simulation-using-DWSIM/C2/Introduction-to-Flowsheeting/English

2025-05-06T05:52:16Z

Snehalathak:

'''Title: Introduction to Flowsheeting'''

'''Author: Priyam Nayak'''

'''Keywords: '''DWSIM''', '''Material stream, simulation, compounds, thermodynamic package, unit systems, vapor phase mole fraction, pressure calculation mode, temperature, molar flow, density, video tutorial.

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''

|| Welcome to this spoken tutorial on ''' Introduction to flowsheeting''' in DWSIM'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to:
* Simulate a '''Mixer'''
* Follow it up with a '''Cooler'''
* Give a '''two-phase feed'''

|-
|| '''Slide Number 3'''

'''System Requirements'''
|| This tutorial is recorded using
* '''DWSIM version 8. 8.0'''
* '''Windows 11 OS'''

But, this process is identical in '''Linux''', '''Mac OS X '''or '''FOSSEE OS on ARM'''.
|-
|| '''Slide Number 4 '''

'''Pre-requisites I'''
|| To practice this tutorial, you should
* have an introductory exposure to '''DWSIM'''.

|-
|| '''Slide Number 5'''

'''Pre-requisites II'''
|| Also, you should know how to:
* add compounds to a '''flowsheet'''
* select '''thermodynamic packages'''
* specify the properties of a '''material''' stream

|-
|| '''Slide Number 6'''

'''Prerequisite Tutorials and Files'''

'''https://spoken-tutorial.org'''
|| The prerequisite tutorials are available on our website.

You can access these tutorials and all the associated files from this site.
|-
|| '''Slide Number 7'''

'''Hover the mouse on the flowsheet image.'''

Flowsheet.png
|| We will develop the '''flowsheet ''' as shown in the figure here.

Two streams are getting mixed in a mixer.

The output from the mixer is getting cooled using a cooler.

The information required to simulate is also given along with the flowsheet.

Use the '''NRTL property package'''.
|-
|| '''Desktop''' >> '''DWSIM'''
|| To open '''DWSIM''', go to the ''' Desktop''' and double-click on the '''DWSIM''' icon.

|-
|| '''File''' >> '''New Chemical Process Model'''
|| Click on '''File '''on the menu bar.

Select '''New Chemical Process Model'''.
|-
|| Point to '''Simulation Configuration Wizard window'''

''' '''Click the '''Next button.'''
|| A '''Simulation Configuration Wizard''' window appears.

Click the '''Next '''button on the lower right corner of the window.
|-
|| Point to '''Compounds''' tab

Type '''Methanol '''in the search bar.

Check the check box under the '''Added '''column.

'''Point to Added Compounds'''
|| We are now in the '''Compounds''' tab.

We will add the compounds present in the flowsheet.

Type '''Methanol''' in the search bar located at the bottom of the '''Compounds''' tab.

Under the '''Added''' column, check the checkbox for '''Methanol'''.

'''Methanol''' is added to the simulation as displayed against the '''Added Compounds'''.
|-
|| Type '''Water '''in the search tab
|| Similarly, add '''Water ''' from '''Chemsep database'''.
|-
|| Point to '''Added Compounds'''.
|| All the compounds required for this simulation are added.

It can be seen in the '''Added Compounds'''.
|-
|| Click on the '''Next '''button at the bottom.
|| Click on the '''Next '''button at the bottom to continue.
|-
|| Point to '''Property Packages'''

'''Property Packages''' >> '''Available Property Package'''

Scroll down to find '''NRTL.'''

Click on '''Add.'''

|| Now comes '''Property Packages'''.

From the '''Available Property Packages''',

Click on '''NRTL'''.

Then click on '''Add.'''

'''NRTL '''has been added under '''Added Property Packages.'''
|-
|| Click on the '''Next '''button at the bottom.
|| Click on the '''Next '''button at the bottom to continue.
|-
|| '''System of Units''' >> '''SI'''.
|| Next option is the '''System of Units'''.

We will''' '''select '''SI'''.

This has the desired system of units according to our problem statement.
|-
|| Click on the '''Next '''button at the bottom.
|| Click on the '''Next '''button at the bottom to continue.
|-
|| '''Behavior''' >> '''Next'''
|| We will not change anything here.

Click on the '''Next''' button at the bottom.
|-
|| '''Undo/Redo Operation''' >> '''Finish'''
|| We will not change anything here.

Click on the '''Finish''' button at the bottom.

This completes configuring the simulation.
|-
|| Point to '''Object Palette'''

Click on the '''Mixers/Splitters '''section.

Click and drag '''Stream Mixer''' to the flowsheet
|| Now, let us add a '''Stream Mixer'''.

Go to the '''Mixers''' or '''Splitters''' section in the '''Object Palette'''.

It is located on the right side of the flowsheet window.

Drag and drop '''Stream Mixer ''' to the flowsheet.
|-
|| Point to '''Stream Mixer''' added to the flowsheet.

Point to material Stream '''1''' and '''2'''.

Point to Material Stream '''3'''.
|| This is the '''Stream Mixer'''.

It has 3 material streams auto-connected to its connection ports.

Material Streams named '''1''' and '''2''' enter the '''Stream Mixer''' as feed streams.

Material Stream named '''3''' leaves the Stream Mixer as the output stream.
|-
|| '''Click >> 1 >> 1 (Material Stream) Property Editor Window.'''

'''Information''' >> '''General Info''' >> '''Object''' >> '''Feed-1'''

Press '''Enter'''
|| Now we will rename all the objects.

Click on the Material Stream named '''1'''.

'''1 (Material Stream)''' property editor window opens.

Under the '''Information '''tab, in the '''General Info''' section, we have ''' Object ''' field.

In this field rename '''1 '''as''' Feed-1''' and press '''Enter.'''
|-
|| '''Click >> 2 >> 2 (Material Stream) Property Editor Window.'''

'''Information''' >> '''General Info''' >> '''Object''' >> '''Feed-2'''
|| Similarly, rename the material stream named '''2 ''' as '''Feed-2'''.
|-
|| '''Click >> 3 >> 3 (Material Stream) Property Editor Window.'''

'''Information''' >> '''General Info''' >> '''Object''' >> '''Mix-Out'''
|| Rename the material stream named '''3 '''as '''Mix-Out'''.

|-
|| '''Click >> Mix-1 >> Mix-1 (Stream Mixer) Property Editor Window'''

'''Information''' >> '''General Info''' >> '''Object''' >> '''Mixer'''
|| Now, rename the mixer object named '''Mix-1 ''' as '''Mixer'''.
|-
|| Cursor near '''Feed stream '''properties.
|| Now we will specify the '''Feed stream''' properties.
|-
|| Click on '''Feed-1.'''

Property editor window opens.
|| Now click on the '''Feed-1'''.

Here, the property editor window opens.
|-
|| '''Input Data>> Stream Conditions >> Flash Spec>> Temperature''' '''and Pressure(TP)'''.

|| Under '''Input Data''', in the '''Stream Conditions''' section, select '''Flash Spec''' as '''Temperature and Pressure (TP).'''

By default, '''Flash Spec ''' is already selected as '''Temperature and Pressure.'''

So let’s not change it.
|-
|| '''Input Data >> Stream Conditions >> Temperature >> 350 K'''

Press '''Enter'''
|| Change '''Temperature''' to '''350 K''' and press '''Enter.'''
|-
|| '''Input Data >> Stream Conditions >> Molar Flow >> 50 mol/s'''

Press '''Enter'''
|| Change '''Molar Flow''' to '''50 mol/s '''and press '''Enter'''.
|-
|| '''Click >> Compound Amounts'''

'''Basis >> Mole Fractions'''
|| Next is to specify the composition of this stream.

To do this, click on '''Compound Amounts'''.

Choose the '''Basis''' as '''Mole Fractions,''' if not already selected.

By default, '''Mole Fractions''' are selected as '''Basis'''.
|-
|| '''Point to the Amount Table.'''

'''Methanol >> 1'''

'''Water >> 0'''
|| Now we will enter the Mole Fractions for each compound.

Click on the first cell below '''Amount''' against '''Methanol '''and enter 1.

Press '''Enter'''.

Similarly, for '''Water, ''' enter it as '''0 '''and press '''Enter.'''

|-
|| '''Click >> Accept changes'''
|| On the right side, click on '''Accept Changes''' button'''.
|-
|| Click on '''Feed-2.'''

Property editor window opens.
|| Now click on the '''Feed-2'''.

Here, the property editor window opens.
|-
|| '''Input Data>> Stream Conditions >> Flash Spec>> Pressure and Vapor Fraction (PVF)'''.

|| Under '''Input Data''', in '''Stream Conditions''' section, select '''Flash Spec''' as '''Pressure and Vapor Fraction (PVF).'''
|-
|| '''Input Data >> Stream Conditions >> Pressure >> 202650 Pa'''

Press '''Enter'''
|| Change '''Pressure ''' to '''202650 Pascals''' and press '''Enter'''.
|-
|| '''Input Data >> Stream Conditions >> Molar Flow >> 50 mol/s'''

Press '''Enter'''
|| Change '''Molar Flow''' to '''50 mol/s ''' and press '''Enter'''.
|-
|| '''Input Data >> Stream Conditions >> Vapor Phase Mole Fraction >> 0.5'''

Press '''Enter'''
|| Change '''Vapor Phase Mole Fraction '''to '''0.5 ''' and press '''Enter.'''
|-
|| '''Click >> Compound Amounts'''

'''Basis >> Mole Fractions'''
|| Next is to specify the composition of this stream.

To do this, click on '''Compound Amounts'''.

Choose the '''Basis''' as '''Mole Fractions,''' if not already selected.

By default, '''Mole Fractions''' are selected as '''Basis'''.
|-
|| '''Point to the Amount Table.'''

Click '''Clear.'''

'''Methanol >> 0'''

'''Water >> 1'''
|| Now we will enter the Mole Fractions for each compound.

Click '''Clear ''' if random values are present.

Click on the first cell below '''Amount''' against '''Methanol '''and enter '''0'''.

Press '''Enter'''.

Similarly, for '''Water, '''enter it as '''1 '''and press '''Enter.'''
|-
|| '''Click >> Accept changes'''
|| On the right, click on '''Accept Changes ''' button'''.

|-
|| Click '''Mixer'''
|| Now we will specify the '''Mixer.'''

Click on '''Mixer.'''

'''Mixer '''property editor window opens.
|-
|| Hover the mouse on '''Calculation Parameters '''
|| Go to the section '''Calculation Parameters ''' by scrolling below.
|-
|| '''Pressure Calculation >> Inlet Maximum'''
|| Click on the drop box against '''Pressure Calculation '''and select '''Inlet Maximum'''.

This will ensure that the outlet stream from the mixer is at 202650 '''Pascals'''.

This is as per the given '''flowsheet'''.
|-
|| Click''' Solve'''
|| Click on the '''Solve''' button in the toolbar area.

The flowsheet is solved till the '''Mix-Out''' stream.

We will proceed further.
|-
|| Click on '''File '''and Click '''Save As'''
|| Let us now save this file till this point.

Click on '''File''' and select '''Save As''' option.
|-
|| Type '''flowsheet-1'''
|| Select a desired location to save the file.

Enter the file name as '''flowsheet-1'''.

It is strongly recommended to save the file intermittently.
|-
|| Point to '''Object Palette'''

Click on the '''Exchangers '''section.

Click and drag '''Cooler''' to the flowsheet

|| Now let us continue with the flowsheet.

Next, we will add a '''Cooler'''.

Go to the '''Exchangers''' section in the '''Object Palette'''.

Scroll down a little to see '''Cooler'''.

Drag and drop '''Cooler ''' to the flowsheet area close to the '''Mix-Out''' stream.
|-
|| '''Click >> CL-1 '''

'''Property Editor Window.'''

'''Information''' >> '''General Info''' >> '''Object''' >> '''Cooler'''
|| Let us rename the newly added objects.

Click on the cooler object named '''CL-1''' and rename it as '''Cooler'''.

Here, the property editor window opens.
|-
|| '''Click >> 5 >> 5 (Material Stream) Property Editor Window.'''

'''Information''' >> '''General Info''' >> '''Object''' >> '''Cool-Out.'''
|| Click on the material stream object named ''' 5 '''and rename it as '''Cool-Out'''.
|-
|| Click '''Cooler.'''

'''Point to the window.'''
|| Now, let us specify the '''Cooler'''.

'''Click on Cooler.'''

'''Cooler '''property editor window opens.
|-
|| Hover mouse on '''Calculation Parameters '''
|| Go to the section '''Calculation Parameters'''.
|-
|| '''Calculation Type >> Outlet Temperature'''
|| Click on the drop down against '''Calculation Type '''and select '''Outlet Temperature'''.

This is because as per the flowsheet, the temperature of the stream coming out of the cooler is mentioned.
|-
|| Efficiency >> 80
|| Click on the field against '''Efficiency''' and enter it as '''80'''.

Press '''Enter'''.
|-
|| Outlet Temperature >> 330 K
|| Click on the field against '''Outlet Temperature'''.

Enter the value as '''330 K'''.

Press '''Enter'''.
|-
|| Click''' Solve'''
|| This completes the flowsheet specification.

Click on the '''Solve''' button in the toolbar area.
|-
||
|| Let us save the flowsheet once again.
|-
|| File >> Save
|| Go to '''File''' and click '''Save'''.
|-

|| '''Insert >> Master Property Table'''
|| Go to the '''Insert ''' menu and select '''Master Property Table'''.
|-
|| Double click on '''Master Property Table'''

Point to '''Configure Master Property Table'''
|| Double-click on the '''Master Property Table ''' to edit it.

'''Configure Master Property Table''' window opens.
|-
||Type '''Steamwise Results – Flowsheet'''
||In the '''Name''' field, type '''Stream Wise Results – Flowsheet'''.
|-
||Select '''Material Stream'''
||In '''Object Type''' select '''Material Stream'''.

By default, '''Material Stream''' is already selected.
|-
||'''Object >> Feed-1, Feed-2, Mix-Out''' and '''Cool-Out'''
||Under '''Properties to display''', select '''Objects''' as '''Feed-1''', '''Feed-2''', '''Mix-Out''' and '''Cool-Out'''.
|-
||'''Configure Master Property Table>> Property'''
||Under '''Property''', scroll down to see all the parameters.

Now select the properties as:

'''Temperature'''

'''Pressure'''

'''Mass Flow'''

'''Molar Flow'''

'''Molar Fraction (Mixture) / Methanol'''

'''Mass Fraction (Mixture) / Methanol'''

'''Molar Flow (Mixture) / Methanol'''

'''Mass Flow (Mixture) / Methanol'''

'''Molar Fraction (Mixture) / Water'''

'''Mass Fraction (Mixture) / Water'''

'''Molar Flow (Mixture) / Water'''

'''Mass Flow (Mixture) / Water'''

|-
||Click on the '''Close''' button.
||Close this window.

Move the '''Master Property Table''' for better visibility.

Here we can see the corresponding results for '''Inlet''' and ''' Outlet Streams.'''
|-
||
|| Let's summarize.
|-
|| '''Slide Number 8'''
'''Summary'''
|| In this tutorial, we have learnt to
* Simulate a '''Mixer'''
* Follow it up with a '''Cooler'''
* Give a '''two-phase feed'''

|-
||'''Slide Number 9'''

''' Assignment'''

Flowsheet-Assignment.png

||As an assignment,

Simulate the given flowsheet.

And use the NRTL property package.
|-
||
|| This brings us to the end of this tutorial.
|-
|| '''Slide Number 10'''

'''About the Spoken Tutorial Project'''
|| Watch the video available at the following link.

[http://spoken-tutorial.org/ https://spoken-tutorial.org/]

It summarises the Spoken Tutorial project.

Please download and watch it
|-
|| '''Slide Number 11'''

'''Spoken Tutorial Workshops'''
||
* The Spoken Tutorial Project Team conducts workshops and gives certificates.
* For more details, please write to us.

|-
|| '''Slide Number 12'''

'''Forum Slide'''

Questions in THIS '''Spoken Tutorial?'''

Visit https://forums.spoken-tutorial.org

Choose the minute and second where you have the question.

Explain your question briefly.

Someone from the FOSSEE team will answer them.

You will have to register on this website to ask questions

|| Do you have questions in THIS Spoken Tutorial?

Please visit this site

Choose the minute and second where you have the question.

Explain your question briefly.

Someone from the FOSSEE team will answer them.

You will have to register on this website to ask questions.

|-
|| '''Slide Number 13'''

'''DWSIM Flowsheeting Project'''

|| The '''FOSSEE''' team coordinates the conversion of existing '''flowsheets''' into '''DWSIM'''.

We give honorarium and certificates for those who do this.

For more details, please visit this site.
|-
|| '''Slide Number 14'''

'''Lab Migration Project'''

|| The '''FOSSEE''' team helps migrate commercial '''simulator labs''' to '''DWSIM.'''

We give honorarium and certificates for those who do this.

For more details, please visit this site
|-
|| '''Slide Number 15'''

'''Acknowledgements'''
|| The '''Spoken Tutorial''' project was established by the '''Ministry of Education(MoE)''', Government of India.

The '''FOSSEE''' project is funded by '''NMEICT, Ministry of Education(MoE)''', Government of India.
|-
|| '''Slide Number 16'''

'''Thank You'''
|| We thank the '''DWSIM''' team for making this as an''' open source software.'''

This is Aditi Gupta along with Priyam Nayak signing off.

Thank you for joining.
|-
|}

ChemCollective-Virtual-Labs/C2/Solution-Transfer-Modes-in-VLabs/English

2025-04-28T12:04:57Z

Snehalathak:

'''Title of script''': '''Solution Transfer Modes in Vlabs'''

'''Author: Dr.Snehalatha Kaliappan'''

'''Keywords: '''Chemistry Virtual labs, workbench, stockroom, Precise transfer, Realistic transfer, Significant transfer, video tutorial.

{| border=1
|-
! align=center | Visual Cue
! align=center | Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
||Welcome to this spoken tutorial on '''Solution Transfer Modes in Vlabs'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
||In this tutorial, we will learn about,

3 different modes of solution transfer in Vlabs

Precise transfer

Significant transfer and

Realistic transfer

|-
|| '''Slide Number 3'''

'''System Requirement'''
||Here I am using,

'''Ubuntu Linux '''OS version 22.04

ChemCollective Virtual labs version 2.1.0

Java version 11.0.5 and

A working internet connection

|-
|| '''Slide Number 4'''

'''Prerequisite'''

||To follow this tutorial,

Learners must be familiar with the ChemCollective Virtual labs interface.
|-
|| Type ChemCollective virtual labs on Google search page.
||For this demonstration I will open the '''ChemCollective Virtual Labs online''' interface.

Open any web browser.

In the Google search, type '''ChemCollective virtual labs '''and press''' Enter.'''
|-
|| '''https://chemcollective.org/vlabs'''
||Click on the '''ChemCollective Virtual labs '''link that appears first on the page.
|-
|| Cursor on the page.

Point to '''Resources Type''': '''Virtual Labs'''.

||By default the main page opens with '''Resource Type''': '''Virtual Labs'''.

List of available topics are listed on the page.
|-
|| Click on '''Stoichiometry''' topic.
||Click on the down arrow next to '''Stoichiometry''' topic.

A menu with the available virtual lab experiments opens.
|-
|| Click on the yellow coloured '''Go''' button.

Cursor on the page.

|| In the''' Glucose Dilution Problem '''activity, click on the '''Go''' button.

'''Glucose Dilution Problem, virtual lab''' page opens.

|-
|| Point to '''Stockroom''' and '''Workbench 1'''.
||Page has two panels: '''Stockroom''' and '''Workbench 1'''.
|-
|| Point to the '''Solutions''', '''Glassware '''and '''Tools''' tabs.
||In the Stockroom, we have '''Solutions''', '''Glassware '''and '''Tools''' tabs.

|-
|| From the '''Stockroom''', click on '''1M Glucose Solution. '''

Cursor on the panel.

Cursor on the Panel.

Point to the information
||From the '''Solutions tab''', click on '''1 Molar Glucose Solution'''.

100 mL of 1 Molar glucose solution is added to the Workbench.

Information about 1 Molar glucose solution is shown in the left panel.
|-
|| From the '''Stockroom''', click on the '''Glassware''' tab.

Click on''' Erlenmeyers'''.

Select 250 ml Erlenmeyer flasks by clicking on the plus button.
||From the '''Stockroom''', click on '''Glassware''' tab.

Select 250 mL '''Erlenmeyer flask''' by clicking on the plus button.

Drag and place the 250 mL flask at a convenient location.
|-
|| Drag the Glucose solution flask to the empty flask
||I want to transfer 1 Molar Glucose solution to an empty flask.

Drag the Glucose solution flask to the empty receiving flask.
|-
|| Cursor on the pop-up window.
||A pop-up window with 3 different modes of transfer appears.
|-
|| '''Slide Number 5'''

'''Precise Transfer'''
||'''Precise '''transfer mode is used to transfer precisely upto second decimal point.

Precise transfer mode can be used for transfer of both solids and liquids.

|-
|| Type 10.546 in the volume field. Click the on '''Pour''' button.
||I will transfer 10.546 mL of solution.

Type 10.546 in the volume field.

Click on the '''Pour''' button.
|-
|| Click on the X button on the right-side of the pop-up window.
||Click on the '''X''' button on the right-side of the pop-up window to close the window.
|-
|| Click on the receiving flask.

Cursor on the left panel.
||Click on the receiving flask.

The left panel shows the volume in the flask as 10.546 ml.
|-
|| Right-click on the flask.

Click the '''Remove Liquid '''option.

Point to the empty flask.

||Let us empty the liquid in the receiving flask.

Right-click on the flask to open the context menu.

From the menu, click the '''Remove Liquid '''option.

The flask is now empty.

|-
|| Cursor on the workbench.
||Now I will demonstrate '''Significant Transfer '''mode.

|-
|| '''Slide Number 6'''

'''Significant Transfer '''

||Significant transfer is used to transfer liquids from or to the glassware which hold a definite volume of liquid.
|-
|| '''Slide Number 7'''

'''Significant Transfer '''

||This mode is used when glassware such as pipette, burette or measuring cylinder are used to transfer liquids.

It can only transfer the maximum amount of liquid the glassware can hold.
|-
|| Click on the 10 ml Pipette from Glassware tab.
||I will select a 10 ml pipette from the '''Glassware''' tab on the left panel.
|-
|| Drag the 10 ml pipette to the Glucose stock solution flask.
||Drag the 10 mL pipette to the Glucose stock solution flask.
|-
|| Cursor on the pop-up window.

Click on the '''Sig Fig''' button.

||The pop-up transfer window appears.

Click on the '''Sig Fig''' button.

Notice the '''Withdraw''' and '''Pour''' buttons.
|-
|| Type 10.00 in the volume field. click on '''Withdraw''' button.

Click on '''X '''button to close the window.
||Since we are using a 10 ml pipette, type 10.00 in the volume field.

Click on the '''Withdraw''' button.

Click on the '''X '''button to close the window.
|-
|| drag the pipette to the receiving flask.
||Now drag the pipette to the receiving flask.

Again the transfer pop-up window appears.

|-
|| Type 10 and now click on the '''Pour '''button.
||Type 10 and now click on the '''Pour '''button.

Notice the error message in the pop-up window.

|-
|| Type 10.00 and click on the '''Pour '''button.
||While pouring, we need to type the decimal figures also.

So type 10.00 and click the '''Pour''' button.

Close the pop-up window.
|-
|| Cursor on the receiving flask,
||Now you can see 10 ml is transferred to the receiving flask.
|-
|| Right-click on the Pipette and select remove.
||To delete the pipette, right-click on the pipette and select '''Remove '''option.
|-
|| Right-click on the flask.

Click on the '''Remove liquid '''option.

||Again empty the liquid in the receiving flask.

Right-click on the flask, click on '''Remove Liquid '''option.

Now I will demonstrate the '''Realistic transfer '''mode .
|-
|| '''Slide Number 8'''

'''Realistic Transfer'''
||In realistic transfer mode, solutions are transferred by holding down the '''Pour''' button.

The longer the Pour button is held down the greater volume of solution is transferred.
|-
|| Drag the flask with Glucose solution on to the empty Erlenmeyer flask.

In the transfer pop-up choose the '''Realistic '''option.
||Bring the flask with '''Glucose''' solution on to the empty Erlenmeyer flask.

In the transfer pop-up choose the '''Realistic '''option.
|-
|| Text Annotation.

Press and hold the '''Hold to pour''' button to transfer the solution
||Press and hold the, '''Hold to Pour''' button to transfer the solution.

Release the button once the desired amount of liquid is transferred.
|-
|| Cursor on the pop-up window.
||The amount of solution transferred is shown in the pop-up window.
|-
|| Click on the '''X '''button to close the window.
||Close the pop-up window.
|-
|| '''Slide Number 9'''

'''Summary'''

In this tutorial, we have learned about 3 different modes of transfer in Vlabs.

Precise transfer

Realistic transfer

Significant transfer
||With this we come to the end of this tutorial.

Let us summarize.

|-
|| '''Slide Number 10'''

'''Assignment'''
||As an assignment,

Practice the transfer of solutions using various transfer modes demonstrated in the tutorial.
|-
||
|| Thank you.
|-
|}

ChemCollective-Virtual-Labs/C2/Solution-Transfer-Modes-in-VLabs/English

2025-04-28T11:45:09Z

Snehalathak:

'''Title of script''': '''Solution Transfer Modes in Vlabs'''

'''Author: Dr.Snehalatha Kaliappan'''

'''Keywords: '''Chemistry Virtual labs, workbench, stockroom, Precise transfer, Realistic transfer, Significant transfer, video tutorial.

{| border=1
|-
! align=center | Visual Cue
! align=center | Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
||Welcome to this spoken tutorial on '''Solution Transfer Modes in Vlabs'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
||In this tutorial, we will learn about,

3 different modes of solution transfer in Vlabs

Precise transfer

Significant transfer and

Realistic transfer

|-
|| '''Slide Number 3'''

'''System Requirement'''
||Here I am using,

'''Ubuntu Linux '''OS version 22.04

ChemCollective Virtual labs version 2.1.0

Java version 11.0.5 and

A working internet connection

|-
|| '''Slide Number 4'''

'''Prerequisite'''

||To follow this tutorial,

Learners must be familiar with the ChemCollective Virtual labs interface.
|-
|| Type ChemCollective virtual labs on Google search page.
||For this demonstration I will open the '''ChemCollective Virtual Labs online''' interface.

Open any web browser.

In the Google search, type '''ChemCollective virtual labs '''and press''' Enter.'''
|-
|| '''https://chemcollective.org/vlabs'''
||Click on the '''ChemCollective Virtual labs '''link that appears first on the page.
|-
|| Cursor on the page.

Point to '''Resources Type''': '''Virtual Labs'''.

||By default the main page opens with '''Resource Type''': '''Virtual Labs'''.

List of available topics are listed on the page.
|-
|| Click on '''Stoichiometry''' topic.
||Click on the down arrow next to '''Stoichiometry''' topic.

A menu with the available virtual lab experiments opens.
|-
|| Click on the yellow coloured '''Go''' button.

Cursor on the page.

|| In the''' Glucose Dilution Problem '''activity, click on the '''Go''' button.

'''Glucose Dilution Problem, virtual lab''' page opens.

|-
|| Point to '''Stockroom''' and '''Workbench 1'''.
||Page has two panels: '''Stockroom''' and '''Workbench 1'''.
|-
|| Point to the '''Solutions''', '''Glassware '''and '''Tools''' tabs.
||In the Stockroom, we have '''Solutions''', '''Glassware '''and '''Tools''' tabs.

|-
|| From the '''Stockroom''', click on '''1M Glucose Solution. '''

Cursor on the panel.

Cursor on the Panel.

Point to the information
||From the '''Solutions tab''', click on '''1 Molar Glucose Solution'''.

100 mL of 1 Molar glucose solution is added to the Workbench.

Information about 1 Molar glucose solution is shown in the left panel.
|-
|| From the '''Stockroom''', click on the '''Glassware''' tab.

Click on''' Erlenmeyers'''.

Select 250 ml Erlenmeyer flasks by clicking on the plus button.
||From the '''Stockroom''', click on '''Glassware''' tab.

Select 250 mL '''Erlenmeyer flask''' by clicking on the plus button.

Drag and place the 250 mL flask at a convenient location.
|-
|| Drag the Glucose solution flask to the empty flask
||I want to transfer 1 Molar Glucose solution to an empty flask.

Drag the Glucose solution flask to the empty receiving flask.
|-
|| Cursor on the pop-up window.
||A pop-up window with 3 different modes of transfer appears.
|-
|| '''Slide Number 5'''

'''Precise Transfer'''
||'''Precise '''transfer mode is used to transfer precisely upto second decimal point.

Precise transfer mode can be used for transfer of both solids and liquids.

|-
|| Type 10.546 in the volume field. Click the on '''Pour''' button.
||I will transfer 10.546 mL of solution.

Type 10.546 in the volume field.

Click on the '''Pour''' button.
|-
|| Click on the X button on the right-side of the pop-up window.
||Click on the '''X''' button on the right-side of the pop-up window to close the window.
|-
|| Click on the receiving flask.

Cursor on the left panel.
||Click on the receiving flask.

The left panel shows the volume in the flask as 10.546 ml.
|-
|| Right-click on the flask.

Click the '''Remove Liquid '''option.

Point to the empty flask.

||Let us empty the liquid in the receiving flask.

Right-click on the flask to open the context menu.

From the menu, click the '''Remove Liquid '''option.

The flask is now empty.

|-
|| Cursor on the workbench.
||Now I will demonstrate '''Significant Transfer '''mode.

|-
|| '''Slide Number 6'''

'''Significant Transfer '''

||Significant transfer is used to transfer liquids from or to the glassware which hold a definite volume of liquid.
|-
|| '''Slide Number 7'''

'''Significant Transfer '''

||This mode is used when glassware such as pipette, burette or measuring cylinder are used to transfer liquids.

It can only transfer the maximum amount of liquid the glassware can hold.
|| Click on the 10 ml Pipette from Glassware tab.
||I will select a 10 ml pipette from the '''Glassware''' tab on the left panel.
|-
|| Drag the 10 ml pipette to the Glucose stock solution flask.
||Drag the 10 mL pipette to the Glucose stock solution flask.
|-
|| Cursor on the pop-up window.

Click on the '''Sig Fig''' button.

||The pop-up transfer window appears.

Click on the '''Sig Fig''' button.

Notice the '''Withdraw''' and '''Pour''' buttons.
|-
|| Type 10.00 in the volume field. click on '''Withdraw''' button.

Click on '''X '''button to close the window.
||Since we are using a 10 ml pipette, type 10.00 in the volume field.

Click on the '''Withdraw''' button.

Click on the '''X '''button to close the window.
|-
|| drag the pipette to the receiving flask.
||Now drag the pipette to the receiving flask.

Again the transfer pop-up window appears.

|-
|| Type 10 and now click on the '''Pour '''button.
||Type 10 and now click on the '''Pour '''button.

Notice the error message in the pop-up window.

|-
|| Type 10.00 and click on the '''Pour '''button.
||While pouring, we need to type the decimal figures also.

So type 10.00 and click the '''Pour''' button.

Close the pop-up window.
|-
|| Cursor on the receiving flask,
||Now you can see 10 ml is transferred to the receiving flask.
|-
|| Right-click on the Pipette and select remove.
||To delete the pipette, right-click on the pipette and select '''Remove '''option.
|-
|| Right-click on the flask.

Click on the '''Remove liquid '''option.

||Again empty the liquid in the receiving flask.

Right-click on the flask, click on '''Remove Liquid '''option.

Now I will demonstrate the '''Realistic transfer '''mode .
|-
|| '''Slide Number 8'''

'''Realistic Transfer'''
||In realistic transfer mode, solutions are transferred by holding down the '''Pour''' button.

The longer the Pour button is held down the greater volume of solution is transferred.
|-
|| Drag the flask with Glucose solution on to the empty Erlenmeyer flask.

In the transfer pop-up choose the '''Realistic '''option.
||Bring the flask with '''Glucose''' solution on to the empty Erlenmeyer flask.

In the transfer pop-up choose the '''Realistic '''option.
|-
|| Text Annotation.

Press and hold the '''Hold to pour''' button to transfer the solution
||Press and hold the, '''Hold to Pour''' button to transfer the solution.

Release the button once the desired amount of liquid is transferred.
|-
|| Cursor on the pop-up window.
||The amount of solution transferred is shown in the pop-up window.
|-
|| Click on the '''X '''button to close the window.
||Close the pop-up window.
|-
|| '''Slide Number 9'''

'''Summary'''

In this tutorial, we have learned about 3 different modes of transfer in Vlabs.

Precise transfer

Realistic transfer

Significant transfer
||With this we come to the end of this tutorial.

Let us summarize.

|-
|| '''Slide Number 10'''

'''Assignment'''
||As an assignment,

Practice the transfer of solutions using various transfer modes demonstrated in the tutorial.
|-
||
|| Thank you.
|-
|}

ChemCollective-Virtual-Labs/C2/Solution-Transfer-Modes-in-VLabs/English

2025-04-23T10:21:29Z

Snehalathak: Created page with " '''Title of script''': '''Solution Transfer Modes in Vlabs''' '''Author: Dr.Snehalatha Kaliappan''' '''Keywords: '''Chemistry Virtual labs, workbench, stockroom, Precise..."

'''Title of script''': '''Solution Transfer Modes in Vlabs'''

'''Author: Dr.Snehalatha Kaliappan'''

'''Keywords: '''Chemistry Virtual labs, workbench, stockroom, Precise transfer, Realistic transfer, Significant transfer, video tutorial.

{| border=1
|-
! align=center | Visual Cue
! align=center | Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
||Welcome to this spoken tutorial on '''Solution Transfer Modes in Vlabs'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
||In this tutorial, we will learn about,

3 different modes of solution transfer in Vlabs

Precise transfer

Significant transfer and

Realistic transfer

|-
|| '''Slide Number 3'''

'''System Requirement'''
||Here I am using,

'''Ubuntu Linux '''OS version 22.04

ChemCollective Virtual labs version 2.1.0

Java version 11.0.5 and

A working internet connection

|-
|| '''Slide Number 4'''

'''Prerequisite'''

||To follow this tutorial,

Learners must be familiar with the ChemCollective Virtual labs interface.
|-
|| Type ChemCollective virtual labs on Google search page.
||For this demonstration I will open the '''ChemCollective Virtual Labs online''' interface.

Open any web browser.

In the Google search, type '''ChemCollective virtual labs '''and press''' Enter.'''
|-
|| '''https://chemcollective.org/vlabs'''
||Click on the '''ChemCollective Virtual labs '''link that appears first on the page.
|-
|| Cursor on the page.

Point to '''Resources Type''': '''Virtual Labs'''.

||By default the main page opens with '''Resources Type''': '''Virtual Labs'''.

List of available topics are listed on the page.
|-
|| Click on '''Stoichiometry''' topic.
||Click on the down arrow next to '''Stoichiometry''' topic.

A menu with the available virtual lab experiments opens.
|-
|| Click on the yellow coloured '''Go''' button.

Cursor on the page.

|| In the''' Glucose Dilution Problem '''activity, click on the '''Go''' button.

'''Glucose Dilution Problem, virtual lab''' page opens.

|-
|| Point to '''Stockroom''' and '''Workbench 1'''.
||Page has two panels: '''Stockroom''' and '''Workbench 1'''.
|-
|| Point to the '''Solutions''', '''Glassware '''and '''Tools''' tabs.
||In the Stockroom, we have '''Solutions''', '''Glassware '''and '''Tools''' tabs.

|-
|| From the '''Stockroom''', click on '''1M Glucose Solution. '''

Cursor on the panel.

Cursor on the Panel.

Point to the information
||From the '''Solutions tab''', click on '''1 Molar Glucose Solution. '''

100 mL of 1 Molar glucose solution is added to the Workbench.

Information about 1 Molar glucose solution is shown in the left panel.
|-
|| From the '''Stockroom''', click on the '''Glassware''' tab.

Click on''' Erlenmeyers'''.

Select 250 ml Erlenmeyer flasks by clicking on the plus button.
||From the '''Stockroom''', click on '''Glassware''' tab.

Select 250 mL '''Erlenmeyer flask''' by clicking on the plus button.

Drag and place the 250 mL flask at a convenient location.
|-
|| Drag the Glucose solution flask to the empty flask
||I want to transfer 1 Molar Glucose solution to an empty flask.

Drag the Glucose solution flask to the empty receiving flask.
|-
|| Cursor on the pop-up window.
||A pop-up window with 3 different modes of transfer appears.
|-
|| '''Slide Number 5'''

'''Precise Transfer'''
||'''Precise '''transfer mode is used to transfer precisely upto second decimal point.

Precise transfer mode can be used for transfer of both solids and liquids.

|-
|| Type 10.546 in the volume field. Click the on '''Pour''' button.
||I will transfer 10.546 mL of solution.

Type 10.546 in the volume field.

Click on the '''Pour''' button.
|-
|| Click on the X button on the right-side of the pop-up window.
||Click on the '''X''' button on the right-side of the pop-up window to close the window.
|-
|| Click on the receiving flask.

Cursor on the left panel.
||Click on the receiving flask.

The left panel shows the volume in the flask as 10.546 ml.
|-
|| Right-click on the flask.

Click the '''Remove Liquid '''option.

Point to the empty flask.

||Let us empty the liquid in the receiving flask.

Right-click on the flask to open the context menu.

From the menu, click the '''Remove Liquid '''option.

The flask is now empty.

|-
|| Cursor on the workbench.
||Now I will demonstrate '''Significant Transfer '''mode.

|-
|| '''Slide Number 6'''

'''Significant Transfer '''

||Significant transfer is used to transfer liquids from or to the glassware which hold a definite volume of liquid.

This mode is used when glassware such as pipette, burette or measuring cylinder are used to transfer liquids.

It can only transfer the maximum amount of liquid the glassware can hold.

|-
|| Click on the 10 ml Pipette from Glassware tab.
||I will select a 10 ml pipette from the '''Glassware''' tab on the left panel.
|-
|| Drag the 10 ml pipette to the Glucose stock solution flask.
||Drag the 10 mL pipette to the Glucose stock solution flask.
|-
|| Cursor on the pop-up window.

Click on the '''Sig Fig''' button.

||The pop-up transfer window appears.

Click on the '''Sig Fig''' button.

Notice the '''Withdraw''' and '''Pour''' buttons.
|-
|| Type 10.00 in the volume field. click on '''Withdraw''' button.

Click on '''X '''button to close the window.
||Since we are using a 10 ml pipette, type 10.00 in the volume field.

Click on the '''Withdraw''' button.

Click on the '''X '''button to close the window.
|-
|| drag the pipette to the receiving flask.
||Now drag the pipette to the receiving flask.

Again the transfer pop-up window appears.

|-
|| Type 10 and now click on the '''Pour '''button.
||Type 10 and now click on the '''Pour '''button.

Notice the error message in the pop-up window.

|-
|| Type 10.00 and click on the '''Pour '''button.
||While pouring, we need to type the decimal figures also.

So type 10.00 and click the '''Pour''' button.

Close the pop-up window.
|-
|| Cursor on the receiving flask,
||Now you can see 10 ml is transferred to the receiving flask.
|-
|| Right-click on the Pipette and select remove.
||To delete the pipette, right-click on the pipette and select '''Remove '''option.
|-
|| Right-click on the flask.

Click on the '''Remove liquid '''option.

||Again empty the liquid in the receiving flask.

Right-click on the flask, click on '''Remove Liquid '''option.

Now I will demonstrate the '''Realistic transfer '''mode .
|-
|| '''Slide Number 7'''

'''Realistic Transfer'''
||In realistic transfer mode, solutions are transferred by holding down the '''Pour''' button.

The longer the Pour button is held down the greater volume of solution is transferred.
|-
|| Drag the flask with Glucose solution on to the empty erlenmeyer flask.

In the transfer pop-up choose the '''Realistic '''option.
||Bring the flask with '''Glucose''' solution on to the empty Erlenmeyer flask.

In the transfer pop-up choose the '''Realistic '''option.
|-
|| Text Annotation.

Press and hold the '''Hold to pour''' button to transfer the solution
||Press and hold the, '''Hold to Pour''' button to transfer the solution.

Release the button once the desired amount of liquid is transferred.
|-
|| Cursor on the pop-up window.
||The amount of solution transferred is shown in the pop-up window.
|-
|| Click on the '''X '''button to close the window.
||Close the pop-up window.
|-
|| '''Slide Number 8'''

'''Summary'''

In this tutorial, we have learned about 3 different modes of transfer in Vlabs.

Precise transfer

Realistic transfer

Significant transfer
||With this we come to the end of this tutorial.

Let us summarize.

|-
|| '''Slide Number 9'''

'''Assignment'''
||As an assignment,

Practice the transfer of solutions using various transfer modes demonstrated in the tutorial.
|-
||
|| Thank you.
|-
|}

Process-Simulation-using-DWSIM/C2/Simulating-a-Material-Stream/English

2025-04-16T10:19:55Z

Snehalathak:

'''Title: Simulating a Material Stream'''

'''Author''': '''Priyam Nayak'''

'''Keywords: '''DWSIM''', '''Material stream, simulation, compounds, thermodynamic package, unit systems, mass fraction, temperature, pressure, molar flow, density, viscosity, thermal conductivity, video tutorial.

{| border=1
|-
|| '''Visual Cue '''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on''' Simulating a Material Stream''' in '''DWSIM'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to:
* Select '''Chemical''' Compounds
* Select a '''Thermodynamic Package''' and '''Unit System'''
* Specify a '''Material Stream'''
* Find '''Thermophysical Properties''' of the '''Material Stream'''

|-
|| '''Slide Number 3'''

'''System Requirements'''
|| This tutorial is recorded using,
* '''DWSIM version 8.8.0'''
* '''Windows 11 OS'''

But, this process is identical in '''Linux''', '''Mac OS X '''or '''FOSSEE OS on ARM'''.
|-
|| '''Slide Number 4'''

'''Pre-requisites'''
|| To follow this tutorial,

You should have '''DWSIM''' installed on your machine.
|-
|| '''Slide Number 5'''

'''Problem Statement - Part I'''
|| Let us determine the following thermophysical properties of a material stream.
|-
|| '''Slide Number 6'''

'''Problem Statement - Part II'''
|| Here we give '''Compounds''', '''Thermodynamics '''and '''Inlet stream conditions.'''
|-
|| '''Desktop''' >> '''DWSIM'''
|| To open '''DWSIM''', go to the''' Desktop''' and double-click on the '''DWSIM icon.'''
|-
|| '''DWSIM''' window opens.
|| '''DWSIM''' window opens.
|-
|| Cursor on the window.
|| Let us start by creating a '''New Chemical Process Model'''.
|-
|| '''File''' >> '''New Chemical Process Model'''
|| Click on '''File '''on the menu bar and select '''New Chemical Process Model'''.
|-
|| Point to '''Simulation Configuration Wizard window'''
|| A '''Simulation Configuration Wizard''' window appears.
|-
|| Click the '''Next button.'''
|| Click the '''Next '''button on the lower right corner of the window.
|-
|| Point to the '''Compounds''' tab
|| We are now in the '''Compounds''' tab.

We will add the compounds available in the flowsheet.
|-
|| Type '''Ethanol '''in the search bar.
|| Type '''Ethanol''' in the search bar at the bottom of the '''Compounds''' tab.
|-
|| Check the check box under the '''Added '''column.
|| Under the '''Added''' column, check the checkbox for '''Ethanol'''.

Alternatively, we can also double-click anywhere on this line to add '''Ethanol'''.
|-
|| Point to '''Added Compounds'''
|| '''Ethanol''' is added to the simulation as displayed against the '''Added Compounds'''.
|-
|| Type '''Water '''in the search tab
|| Similarly, add '''Water '''from '''Chemsep Database'''.
|-
|| Point to '''Added Compounds'''.
|| All the compounds required for this simulation are now added.

This can be seen in the '''Added Compounds'''.
|-
|| Click on the '''Next '''button at the bottom.
|| Click on the '''Next '''button at the bottom to continue.
|-
|| Point to '''Property Packages'''
|| Now comes the '''Property Packages'''.

Based on the compounds added, '''DWSIM '''suggests a list of '''Property Packages''' applicable to the system.

This suggestion may not always be right.

Users must make an informed decision using the basics of thermodynamics.

This will help them to select a property package.

For this problem, it has been specified that '''NRTL''' has to be selected.

'''Non-Random Two-Liquid''' model is abbreviated as NRTL.

It is useful for calculating activity coefficients in non-ideal solutions.
|-
|| '''Property Packages''' >> '''Available Property Package'''

Click '''NRTL.'''
|| From the '''Available Property Packages''',

click on '''NRTL.'''
|-
|| Click on '''Add'''.
|| Then click on the '''Add '''button.
|-
|| Point to '''Added Property Packages.'''
|| '''NRTL '''has been added under '''Added Property Packages'''.

Alternatively, we can also double-click on '''NRTL '''to add it.
|-
|| Click the '''Next button.'''
|| Click the '''Next''' button at the bottom'''.'''
|-
|| Point to '''System of Units'''
|| The next option is the '''System of Units.'''
|-
|| Click on the drop-down against '''System of Units'''.
|| Click on the drop-down against '''System of Units'''.
|-
|| Hover mouse on list shown at the drop-down
|| Here, we can see the different '''System of Units''' available with '''DWSIM'''.
|-
|| Hover mouse on '''SI''', '''CGS,''' and '''ENG.'''
|| '''SI''', '''CGS,''' and '''ENG''' are the different standard systems of units used for measurement.
|-
|| Hover mouse at '''SI (Engineering)''', '''C1, C2, C3, C4''' and '''C5.'''
|| '''SI (Engineering), C1, C2, C3, C4''' and '''C5 '''are custom systems of units.

'''C1, C2, C3, C4,''' and '''C5''' can be modified as per the simulation problem requirement.
|-
|| '''System of Units >> SI'''
|| As per the given simulation problem statement, '''SI '''is the best-suited '''System of Units'''.

Select '''SI '''from the drop-down.
|-
|| Click on '''Next.'''
|| Click on the '''Next '''button at the bottom.
|-
|| Point to the '''Behavior''' window.
|| The next window is '''Behavior'''.

This is to make some changes in the way in which''' DWSIM''' behaves currently.

We will not change anything here.
|-
|| '''Behavior''' >> '''Next'''
|| Click on the '''Next''' button at the bottom.
|-
|| Point to '''Undo/Redo Operations'''
|| This is the '''Undo/Redo Operations''' Window.

It is to enable the '''Undo/Redo''' capabilities.

We will not change anything here.
|-
|| '''Undo/Redo Operations''' >> '''Finish'''
|| Click on the '''Finish''' button at the bottom.

This completes configuring the simulation.
|-
|| Click and drag '''Material Stream''' to flowsheet
|| Go to the '''Streams '''tab.

Drag and drop a '''Material Stream''' from the displayed list to the '''Flowsheet area'''.
|-
|| Cursor at the stream.
|| Let us arrange the '''Stream'''.
|-
|| Clicking on the '''Stream, Property Editor Window '''opens.

Hover the mouse over the '''Property Editor Window'''
|| We click on the '''Stream, '''the '''Property Editor Window '''opens.

We see the '''Property Editor Window''' on the left-hand side of the '''Flowsheet'''.

|-
|| Type '''Object''' as '''Feed.'''
|| Let us rename the '''material stream''' first.

Under '''General Info''', type the '''Object''' as '''Feed'''.

Press''' Enter.'''

In '''DWSIM''', after every change, ensure to press '''Enter''' for the change to be effective.
|-
|| Point to '''Input Data'''

Cursor to the default values
|| The '''Input Data''' tab shows all the properties of the stream.

'''DWSIM '''assigns default values to all properties.
|-
|| Point to '''Flash Spec'''

Click on drop-down against '''Flash Spec'''
|| Under '''Stream Conditions '''tab, the first option is to specify the '''Flash Spec'''.

We can select one of the '''Flash Spec'''s depending on the data given.
|-
|| '''Slide Number 5'''

'''Problem Statement - Part I'''
|| Let me go back to the slides.

Here, '''Temperature ''' and '''Pressure''' data is given in the problem statement.
|-
|| '''Stream Conditions >> Flash Spec >> Select Temperature and Pressure (TP)''' from the Drop down.

Point to '''Temperature '''and''' Pressure.'''

|| Select '''Flash Spec''' as '''Temperature and Pressure (TP)''' if not already selected.

By default, '''Temperature '''and''' Pressure '''is already selected as '''Flash Spec.'''
|-
|| '''Input Data >> Temperature >> 320 K'''

Press '''Enter'''
|| Next is to specify the '''Temperature'''.

Change '''Temperature''' to '''320 Kelvin '''and press '''Enter.'''
|-
|| '''Input Data >> Pressure >> 202650 Pa'''

Press '''Enter'''
|| Next is to specify the '''Pressure'''.

Change '''Pressure''' to '''202650 Pa''' and press '''Enter'''.
|-
|| Hover Mouse at '''Mass Flow, Molar Flow''' and '''Volumetric Flow.'''
|| Next is to specify the '''Flow Rate'''.

Here, out of the '''Mass Flow''', '''Molar Flow''' and '''Volumetric Flow''', only one has to be specified.

Other two will be calculated accordingly.
|-
|| '''Input Data >> Molar Flow >> 500 mol/s'''

Press '''Enter'''
|| As per the problem statement, molar flow is given as '''500 mol/s'''.

Change '''Molar Flow''' to '''500 mol/s''' and press '''Enter.'''
|-
|| '''Cursor near the material stream.'''
|| Now let us specify the '''material stream''' compositions.
|-
|| '''Input Data >> Compound Amounts'''
|| Under '''Input Data, '''click on the '''Compound Amounts''' tab.
|-
|| Click on the drop-down against '''Basis.'''
|| Click on the drop-down against '''Basis'''.

Here we can specify composition in these ways.
|-
|| '''Compound Amounts >> Basis >> Mass Fractions'''
|| As per the problem statement, the composition is specified in terms of '''mass fraction'''.

Choose the '''Basis ''' as '''Mass Fractions.'''

By default, '''Mole Fractions''' is selected as '''Basis.'''

Let us change this to '''Mass Fractions'''.
|-
|| Point to the '''Amount Table.'''
|| Now we will enter the '''Mass Fractions''' for each compound.
|-
|| '''Ethanol: 0.35'''
|| For '''Ethanol''', enter the '''Amount''' as '''0.35''' and press '''Enter.'''
|-
|| '''Water: 0.65'''
|| For '''Water''', enter '''0.65''' and press '''Enter'''.
|-
|| Click '''Accept Changes'''
|| On the right, click on the '''Accept Changes''' button.
|-
|| Point to '''Basis'''
|| If the total is not 1, '''DWSIM ''' normalises the entries, so that the total becomes 1.

Also, the '''Mass Fractions''' entered are converted to '''Mole Fractions''', which is the default basis.
|-
|| Click''' Solve'''
|| This completes the problem specification.

Click on the '''Solve''' button in the toolbar area.
|-
|| Click on '''Results'''
|| Let us see some of the thermophysical properties of the stream.

Click on the '''Results''' tab next to ''' Input Data.'''
|-
|| '''Results >> Phase Properties'''
|| Under '''Results''', click on '''Phase Properties'''.
|-
|| Click on '''Overall Liquid'''.
|| Click on '''Overall Liquid'''.

Scroll Down to see the different thermophysical properties of the liquid phase.
|-
|| Hover the mouse at different properties
|| You can see values of different properties like:

* Density
* Dynamic Viscosity
* Heat Capacity (Cp)
* Kinematic Viscosity
* Molar Enthalpy

|-
|| Click on '''File '''and Click '''Save As'''
|| Let us now save this file.

To do this, click on '''File''' and then click the '''Save As''' option.
|-
|| Type '''stream'''
|| Select a desired location to save the file and enter the file name as '''stream'''.
|-
|| '''Close the Property Editor Window.'''
|| Close the '''Property Editor Window'''.
|-
|| Click on the''' Material''' Stream
|| We can always get back to the property editor window by clicking on the object.
|-
|| Only Narration.
|| This brings us to the end of this tutorial.

Let's summarize.
|-
|| '''Slide Number 7'''

'''Summary'''
|| In this tutorial, we have learnt to Select '''Chemical''' compounds
* Select a '''Thermodynamic package''' and '''Unit System'''
* Specify a '''Material stream'''
* Find '''Thermophysical Properties''' of '''Material Stream'''

|-
||
|| Here are some assignments for you.
|-
|| '''Slide Number 8'''

'''Assignment 1'''

|| Choose '''Ethanol''' and '''Water mole fractions''' that do not add up to 1.

Check how '''DWSIM '''normalises when you press '''Accept Changes''' button.
|-
|| '''Side Number 9'''

'''Assignment 2 '''
|| Go to the page where you defined '''mole fractions.'''

Check what the '''Normalize''' button does when the '''Total''' is not 1.
|-
|| '''Slide Number 10'''

'''Assignment 3 '''
|| Go to the page where we defined the '''molar flow rate'''.

'''DWSIM''' automatically displays equivalent '''flow rates''' in mass flow and volumetric flow.

Check if these values are consistent.
|-
|| '''Slide Number 11'''

'''Assignment 4 '''
|| Create a '''stream''' consisting of '''Methanol, Ethanol '''and '''Water.'''

Carry out the previous assignments for this '''stream''' also.
|-

|| '''Slide Number 12'''

'''About the Spoken Tutorial Project'''
|| Watch the video available at the following link.

[http://spoken-tutorial.org/ https://spoken-tutorial.org/]

It summarises the Spoken Tutorial project.

Please download and watch it
|-
|| '''Slide Number 13'''

'''Spoken Tutorial Workshops'''
|| The Spoken Tutorial Project Team conducts workshops and gives certificates.

For more details, please write to us.
|-
|| '''Slide Number 14'''

'''Forum Slide'''

Questions in THIS '''Spoken Tutorial?'''

Visit https://forums.spoken-tutorial.org

Choose the minute and second where you have the question.

Explain your question briefly.

Someone from the FOSSEE team will answer them.

You will have to register on this website to ask questions

|| Do you have questions in THIS Spoken Tutorial?

Please visit this site

Choose the minute and second where you have the question.

Explain your question briefly.

Someone from the FOSSEE team will answer them.

You will have to register on this website to ask questions

|-
|| '''Slide Number 15'''

'''DWSIM Flowsheeting Project'''
|| The '''FOSSEE''' team coordinates the conversion of existing '''flowsheets''' into '''DWSIM'''.

We give honorarium and certificates for those who do this.

For more details, please visit this site.
|-
|| '''Slide Number 16'''

'''Lab Migration Project'''
|| The '''FOSSEE''' team helps migrate commercial '''simulator labs''' to '''DWSIM.'''

We give honorarium and certificates for those who do this.

For more details, please visit this site
|-
|| '''Slide Number 17'''

'''Acknowledgements'''
|| The '''Spoken Tutorial''' project was established by the '''Ministry of Education(MoE)''', Government of India.

The '''FOSSEE''' project is funded by '''NMEICT, Ministry of Education(MoE)''', Government of India.
|-
|| '''Slide Number 18'''

'''Thank You'''
|| We thank the '''DWSIM''' team for making it as an''' open source software.'''

This is Aditi Gupta along with Priyam Nayak signing off.

Thank you for joining.
|-
|}

Jmol-Application/C3/Display-Lone-Pair-of-Electrons/English

2025-03-26T10:29:54Z

Snehalathak:

{|border=1
|-
! align=center | Visual Cue
! align=center | Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this Spoken Tutorial on '''Display Lone Pair of Electrons''' in '''Jmol'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Display '''lone pair''' of electrons on an atom using script commands.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| Here I am using,
* '''Ubuntu Linux '''OS version 22.04
* '''Jmol''' version 16.2.35
* '''Java '''version 11.0.25
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''
|| To follow this tutorial,
* learner must be familiar with basic operations on '''Jmol''' interface.
* Spoken tutorials on '''Jmol Application''' are available at the following website.
|-
|| Cursor on '''Jmol''' interface.

Click on the '''File''' menu and select '''Get Mol''' option.

In the input box, type '''water'''.

Click '''OK'''.
|| Open the '''Jmol''' interface.

Click on the '''File''' menu and select '''Get MOL''' option.

In the input box, type '''water''' and Click '''OK'''.
|-
|| Cursor on the panel.

Hold '''Ctrl''' and '''Alt''' keys
|| '''3D''' structure of water is seen on the panel.

Hold '''Ctrl''' and '''Alt''' keys to move the model on the screen.
|-
|| Cursor on the panel.
|| Water has two '''lone''' pairs of '''electrons''' on the '''Oxygen''' atom.

They are also referred to as an '''unshared''' pair of valence '''electrons'''.
|-
|| Cursor on the panel.
|| Using the script commands we can represent '''lone''' pair of '''electrons''' as tear-drop shaped lobes.
|-
|| Click on the '''File''' menu and select the Console option.
|| To open the '''console''' click the '''File''' menu.

Select '''Console''' option.
|-
|| Cursor on the panel.
|| '''Script console''' opens as a pop-up window.
|-
|| Cursor on the console.
|| Here we can write commands to draw the lone pair of electrons.
|-
|| At the prompt, Type the following, '''select oxygen;lcaocartoon color translucent white create lpa'''

Press '''Enter'''.
|| At the prompt, Type the command:

'''select oxygen;lcaocartoon color translucent white create lpa'''

This command will create a translucent white colored lobe on the oxygen atom.

Press '''Enter'''.
|-
|| Cursor on the panel.
|| The first '''lobe''' is seen on the oxygen atom on the panel.

You can change the color in the command according to your preference.
|-
|| Press up arrow key on the keyboard.
|| I will change the color of the '''lobes''' to yellow.

Press the up arrow key to get the previous command at the prompt.
|-
|| '''select oxygen;lcaocartoon color yellow create lpa'''
|| Edit the command and change, '''translucent white''' to '''yellow '''and press '''Enter'''.
|-
||Press the up arrow on the keyboard.

At the end of the command line, change '''lpa '''to '''lpb'''.

Press '''Enter'''.
|| For the second '''lobe''':

Press the up arrow key on the keyboard to get the previous command at the prompt.

Edit the command.

At the end of the command line, change '''lpa '''to '''lpb'''.

Press '''Enter'''.
|-
|| Cursor on the panel.
|| Now we can see two lobes representing two '''lone''' '''pairs''' of '''electrons''' on the panel.
|-
|| Cursor on the panel.
|| I have loaded the '''3D''' structure of '''ammonia''' using '''GetMOL'''.

To open the '''console''' click the '''File''' menu.

Select '''Console''' option.
|-
|| '''Cursor on the console'''

'''select nitrogen;lcaocartoon color yellow create lpa'''.

|| Here is the command line for displaying a '''lone pair''' of electrons on nitrogen in '''ammonia'''.
|-
|| '''Slide Number 5'''

'''Summary'''
|| Let us summarize.

In this tutorial, we have learned to,
* Display '''lone pair''' of electrons on an atom using script commands.
|-
|| '''Slide Number 6'''

'''Assignment'''
|| As an assignment,
* Display a '''lone pair''' of electrons on the phosphorus atom in the phosphine model.
|-
|| '''Slide Number 7'''

'''About Spoken Tutorial Project '''
|| This video summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|| '''Slide Number 8'''

'''Spoken tutorial workshops '''
|| We conduct workshops and give certificates.

For more details, please contact us.
|-
|| '''Slide Number 9'''

'''Forum '''
|| Please post your timed queries in this forum.
|-
|| '''Slide Number 10'''

'''Acknowledgement '''
|| The''' Spoken Tutorial '''project was established at IIT Bombay by the Ministry of Education Govt of '''India.'''
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

Jmol-Application/C2/Interchange-the-Element-in-the-3D-Model/English

2025-03-26T10:16:38Z

Snehalathak:

{|border=1
|-
! align=center | Visual Cue
! align=center | Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
||Welcome to this Spoken Tutorial on '''Interchange the Element In the 3D Model'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Change the element in the 3D model to create a different molecule.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| Here I am using,
*'''Ubuntu Linux ''' OS version 22.04
*'''Jmol''' version 16.2.35
*'''Java''' version 11.0.25
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''
||To follow this tutorial,
* Learner must be familiar with basic operations in '''Jmol''' interface.
*Spoken tutorials on '''Jmol Application''' are available at this website.
|-
|| Click on the model-kit icon.

Cursor on Methane model
|| I have opened the '''Jmol ''' interface.

Click on the '''model kit''' menu to open it.

We have a model of methane on the screen.
|-
|| Cursor on the methane molecule.

Cursor on the elements menu.
|| I would like to change the'''methane '''molecule to '''borane'''.

Here, we need to change the central carbon atom to boron.

Open the '''Model kit''' menu.

In the list of elements boron is not included.

Hence we need to add boron to the list of elements.
|-
|| Click on the double-question mark icon.

type the symbol for boron as capital “B”. Click on OK.
|| Click on the double-question mark icon.

In the '''Element input '''box, type the symbol for boron as capital “'''B'''”.

Click on '''OK'''.
|-
|| Cursor on the menu.
||When you open the '''model-kit''' menu again, boron is already selected.
|-
|| Click on the central carbon atom in the methane model.

Cursor on the boron atom.

|| Now click on the central carbon atom in the methane model.

The carbon is now replaced by boron atom.

You can see the change in the color of the atom to pink.

The valency is automatically adjusted to 3.

Hence you will see 3 hydrogens on central boron atom.
|-
|| Cursor on the borane model.

Click on minimize in the '''model'''-'''kit''' menu.

Select '''exit modelkit mode''' to close the model kit menu.
|| This molecule is borane.

Click on '''minimize''' in the '''model'''-'''kit''' menu to do energy minimization.

Now select '''exit model-kit mode''' to close the model kit menu.
|-
||Double click on any hydrogen atom.

Click on the central boron atom.

Again double-click on the other hydrogen atom.

Cursor on the measurements on the model.
|| Let us measure the bond angle.

Double clicking on any hydrogen atom.

Click on the central boron atom.

Again double-click on the other hydrogen atom.

You can see the bond-angle as 120 degrees .

This corresponds to the '''sp2''' hybridization found in borane.
|-
|| Cursor on the panel.

Click on the '''model kit''' icon.
|| I would now like to change the central atom to silicon to create Silane.

Open the '''model kit''' menu.

Let us add a silicon symbol to the list of elements.
|-
|| Click on the double-question mark icon.

type the symbol for boron as capital “Si”.

Click on OK.
|| Type “'''Si'''” in the element input box and click '''OK'''.
|-
|| Click on the central boron atom on the panel.
|| Now click on the central boron atom on the panel.

Observe the color change of silicon atom.

It is seen as light brown in color.
|-
|| Cursor on the panel.
|| The valency of silicon is 4.

Hence the hydrogens are also adjusted automatically to 4.

This molecule is silane.
|-
|| Click on minimize in the model-kit menu.
|| Click on '''minimize''' in the '''model-kit '''menu to do energy minimization.

Now select '''exit modelkit mode''' to close the model kit menu.

Let us measure the bond angle.
|-
|| Click on '''model''' '''kit''' menu. Select nitrogen from the element list . Click on central silicon atom.
|| Following the same steps I have converted the silane model to ammonia.

Let us measure the bond angle.

In this way we can create '''3D''' models of a number of covalent inorganic molecules.
|-
|| '''Slide Number 5'''

'''Summary '''
|| Let's summarize

In this tutorial,
* We have changed the element of the central atom in the '''3D''' model to create a different molecule.
|-
|| '''Slide Number 6'''

'''Assignment'''
|| As an assignment,

Create models of Phosphine and hydrogen fluoride from model of methane

Measure the bond angle
|-
|| '''Slide Number 7'''

'''About Spoken Tutorial Project '''
|| This video summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|| '''Slide''' '''Number 8'''

'''Spoken tutorial workshops '''
|| We conduct workshops using spoken tutorials and give certificates.

For more details, please write to us.
|-
|| '''Slide Number 9'''

'''Forum '''
|| Please post your timed queries in this forum.
|-
|| '''Slide''' '''Number 10'''

'''Acknowledgement '''
|| The''' Spoken Tutorial '''project was established at IIT Bombay by the Ministry of Education Govt of '''India'''.
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

Jmol-Application/C3/Display-Lone-Pair-of-Electrons/English

2025-03-24T06:46:04Z

Snehalathak: Created page with " {|border=1 |- ! align=center | Visual Cue ! align=center | Narration |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this Spoken Tutorial on '''Display Lone Pai..."

{|border=1
|-
! align=center | Visual Cue
! align=center | Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this Spoken Tutorial on '''Display Lone Pair of Electrons''' in '''Jmol'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Display '''lone''' '''pair''' of electrons on an atom using script commands.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| Here I am using,
* '''Ubuntu Linux '''OS version 22.04
* '''Jmol''' version 16.2.35
* '''Java '''version 11.0.25
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''
|| To follow this tutorial,
* Learner must be familiar with basic operations on '''Jmol''' interface.
* Spoken tutorials on '''Jmol Application''' are available at the following website.
|-
|| Cursor on '''Jmol''' interface.

Click on the '''File''' menu and select '''Get M'''ol option.

In the input box, type '''water. '''

Click '''OK'''.
|| Open the '''Jmol''' interface.

Click on the '''File''' menu and select '''Get Mol''' option.

In the input box, type '''water''' and Click '''OK.'''
|-
|| Cursor on the panel.

Hold '''Ctrl''' and '''Alt''' keys
|| '''3D''' structure of water is seen on the panel.

Hold '''Ctrl''' and '''Alt''' keys to move the model on the screen.
|-
|| Cursor on the panel.
|| Water has two '''lone''' pairs of '''electrons''' on the '''Oxygen''' atom.

They are also referred to as an '''unshared''' pair of valence '''electrons'''.
|-
|| Cursor on the panel.
|| Using the script commands we can represent '''lone''' pair of '''electrons''' as '''tear'''-'''drop''' shaped '''lobes'''.
|-
|| Click on the '''File''' menu and select the Console option.
|| To open the console click the '''File''' menu.

Select '''Console''' option.
|-
|| Cursor on the panel.
|| Script console opens as a pop-up window.
|-
|| Cursor on the console.
|| Here we can write commands to draw the lone pair of electrons.
|-
|| At the prompt, Type the following, '''select oxygen;lcaocartoon color translucent white create lpa'''

Press '''Enter'''.
|| At the prompt, Type the command:

'''select oxygen;lcaocartoon color translucent white create lpa'''

This command will create a translucent white colored lobe on the oxygen atom.

Press '''Enter'''.
|-
|| Cursor on the panel.
|| The first '''lobe''' is seen on the oxygen atom on the panel.

You can change the color in the command according to your preference.
|-
|| Press up arrow key on the keyboard.
|| I will change the color of the '''lobes''' to yellow.

Press the up arrow key to get the previous command at the prompt.
|-
|| '''select oxygen;lcaocartoon color yellow create lpa'''
|| Edit the command and change, '''translucent white''' to '''yellow '''and press '''Enter'''.
|-
||
Press the up arrow on the keyboard.

At the end of the command line, change '''lpa '''to '''lpb'''.

Press '''Enter'''.
|| For the second '''lobe''':

Press the up arrow key on the keyboard to get the previous command at the prompt.

Edit the command.

At the end of the command line, change '''lpa '''to '''lpb'''.

Press '''Enter'''.
|-
|| Cursor on the panel.
|| Now we can see two lobes representing two '''lone''' '''pairs''' of '''electrons''' on the panel.
|-
|| Cursor on the panel.
|| I have loaded the '''3D''' structure of '''ammonia''' using '''GetMol'''.

To open the console click the '''File''' menu.

Select '''Console''' option.
|-
|| '''Cursor on the console'''

'''select nitrogen;lcaocartoon color yellow create lpa'''
|| Here is the command line for displaying a '''lone''' '''pair''' on nitrogen in '''ammonia'''.
|-
|| '''Slide Number 5'''

'''Summary'''
|| Let us summarize.

In this tutorial, we have learned to,
* Display '''lone''' '''pair''' of electrons on an atom using script commands.
|-
|| '''Slide Number 6'''

'''Assignment'''
|| As an assignment,
* Display a '''lone''' '''pair''' of electrons on the phosphorus atom in the phosphine model.
|-
|| '''Slide Number 7'''

'''About Spoken Tutorial Project '''
|| This video summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|| '''Slide Number 8'''

'''Spoken tutorial workshops '''
|| We conduct workshops and give certificates.

For more details, please contact us.
|-
|| '''Slide Number 9'''

'''Forum '''
|| Please post your timed queries in this forum.
|-
|| '''Slide Number 10'''

'''Acknowledgement '''
|| The''' Spoken Tutorial '''project was established at IIT Bombay by the Ministry of Education Govt of '''India.'''
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

Jmol-Application/C2/Interchange-the-Element-in-the-3D-Model/English

2025-03-21T10:56:52Z

Snehalathak: Created page with " {|border=1 |- ! align=center | Visual Cue ! align=center | Narration |- || '''Slide Number 1''' '''Title Slide''' ||Welcome to this Spoken Tutorial on '''Interchange the Ele..."

{|border=1
|-
! align=center | Visual Cue
! align=center | Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
||Welcome to this Spoken Tutorial on '''Interchange the Element In the 3D Model'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,
* Change the element in the 3D model to create a different molecule.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| Here I am using,
*'''Ubuntu Linux '''OS version 22.04
*'''Jmol''' version 16.2.35
*'''Java''' version 11.0.25
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''
||To follow this tutorial,
* Learner must be familiar withBasic operations in '''Jmol''' interface.
*Spoken tutorials on '''Jmol Application''' are available at thiswebsite.
|-
|| Click on the model-kit icon.

Cursor on Methane model
|| I have opened the '''Jmol '''interface.

Click on the '''model kit''' menu to open it.

We have a model of methane on the screen.
|-
|| Cursor on the methane molecule.

Cursor on the elements menu.
|| I would like to change the'''methane '''molecule to borane.

Here, we need to change the central carbon atom to boron.

Open the '''Model kit''' menu.

In the list of elements boron is not included.

Hence we need to add boron to the list of elements.
|-
|| Click on the double-question mark icon.

type the symbol for boron as capital “B”. Click on OK.
|| Click on the double-question mark icon.

In the '''Element input '''box, type the symbol for boron as capital “'''B'''”.

Click on '''OK'''.
|-
|| Cursor on the menu.
||When you open the '''model'''-'''kit''' menu again, boron is already selected.
|-
|| Click on the central carbon atom in the methane model.

Cursor on the boron atom.

|| Now click on the central carbon atom in the methane model.

The carbon is now replaced by boron atom.

You can see the change in the color of the atom to pink.

The valency is automatically adjusted to 3.

Hence you will see 3 hydrogens on central boron atom.
|-
|| Cursor on the borane model.

Click on minimize in the '''model'''-'''kit''' menu.

Select '''exit modelkit mode''' to close the model kit menu.
|| This molecule is borane.

Click on '''minimize''' in the '''model'''-'''kit''' menu to do energy minimization.

Now select '''exit modelkit mode''' to close the model kit menu.
|-
||Double click on any hydrogen atom.

Click on the central boron atom.

Again double-click on the other hydrogen atom .

Cursor on the measurements on the model.
|| Let us measure the bond angle.

Double clicking on any hydrogen atom.

Click on the central boron atom.

Again double-click on the other hydrogen atom .

You can see the bond-angle as 120 degrees .

This corresponds to the '''sp2''' hybridization found in borane.
|-
|| Cursor on the panel.

Click on the '''model kit''' icon.
|| I would now like to change the central atom to silicon to create Silane.

Open the '''model kit''' menu.

Let us add a silicon symbol to the list of elements.
|-
|| Click on the double-question mark icon.

type the symbol for boron as capital “Si”.

Click on OK.
|| Type “'''Si'''” in the element input box and click '''OK'''.
|-
|| Click on the central boron atom on the panel.
|| Now click on the central boron atom on the panel.

Observe the color change of silicon atom.

It is seen as light brown in color.
|-
|| Cursor on the panel.
|| The valency of silicon is 4.

Hence the hydrogens are also adjusted automatically to 4.

This molecule is Silane.
|-
|| Click on minimize in the model-kit menu.
|| Click on '''minimize''' in the '''model'''-'''kit '''menu to do energy minimization.

Now select '''exit modelkit mode''' to close the model kit menu.

Let us measure the bond angle.
|-
|| Click on '''model''' '''kit''' menu. Select Nitrogen from the element list . Click on central silicon atom.
|| Following the same steps I have converted the Silane model to ammonia.

Let us measure the bond angle.

In this way we can create '''3D''' models of a number of covalent inorganic molecules.
|-
|| '''Slide Number 5'''

'''Summary '''
|| Let's summarize

In this tutorial,
* We have changed the element of the central atom in the '''3D''' model to create a different molecule.
|-
|| '''Slide Number 6'''

'''Assignment'''
|| As an assignment,

Create models of Phosphine and Hydrogen fluoride from model of methane

Measure the bond angle
|-
|| '''Slide Number 7'''

'''About Spoken Tutorial Project '''
|| This video summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|| '''Slide''' '''Number 8'''

'''Spoken tutorial workshops '''
|| We conduct workshops using spoken tutorials and give certificates.

For more details, please write to us.
|-
|| '''Slide Number 9'''

'''Forum '''
|| Please post your timed queries in this forum.
|-
|| '''Slide''' '''Number 10'''

'''Acknowledgement '''
|| The''' Spoken Tutorial '''project was established at IIT Bombay by the Ministry of Education Govt of '''India.'''
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Installation-of-AutoDock4-on-Windows-OS-and-macOS/English

2025-01-24T10:34:21Z

Snehalathak:

'''Title of script''': Installation of AutoDock on Windows and mac

'''Author''': Dr. Snehalatha Kaliappan

'''Keywords''': AutoDock4, AutoDock installation, AutoDock Tools, MGL Tools, Windows OS, macOS, video tutorial.

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Installation of AutoDock4 on Windows OS and macOS'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''AutoDock4''' on '''Windows OS'''

Download and install '''MGLTools'''

Check the installation of '''AutoDockTools '''
|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| We will also,

Download and install '''AutoDock4''' on '''macOS'''

Download and install '''XQuartz''' version 2.8.5

|-
|| '''Slide Number 4'''

'''Learning Objectives'''
||
Download and install '''MGLTools'''

Check the installation of '''AutoDockTools''' on '''macOS'''

|-
|| '''Slide Number 5'''

'''System Requirement'''
|| Here I am using

'''Windows 11'''

'''Mac OS''' version 14.5

'''AutoDock''' version 4.2.6

'''MGLTools''' version 1.5.7

'''XQuartz ''' version 2.8.5

'''Firefox ''' web browser version 130.0.1

A working internet connection
|-
|| '''Slide Number 6'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

basic computer operations on '''Windows''' and '''macOS'''
|-
|| Open Firefox web browser.

In the Google search field type, '''AutoDock download''' and press enter.
|| I have opened a google search page in a web browser.

In the Google search field type, '''AutoDock download''' and press Enter.
|-
|| On the google results page,

Click on the first link, '''Download AutoDock4'''

https://autodock.scripps.edu/download-autodock4/
|| A page opens with many results.

Click on the first link, '''Download AutoDock4'''.
|-
|| Cursor on the AutoDock downloads page.
|| This takes you to the '''Autodock download page of Scripps.edu'''.

|-
|| Cursor on the AutoDock downloads page.

[https://autodock.scripps.edu/download-autodock4/ https://autodock.scripps.edu/download-autodock4/]

Click on '''Autodock4 Windows installer file.'''
|| Here, in the center of the page you will see link to installers for various operating systems.

I will click on '''Autodock4 Windows''' installer file.
|-
|| Cursor on the download progress bar at the bottom.
|| '''autodocksuite-4.2.6.i86Windows.exe '''file gets downloaded to your '''Downloads''' folder.
|-
|| Go to the '''Downloads '''folder.

Double click on the downloaded '''autodocksuite-4.2.6.i86Windows.exe '''file.

|| Go to the '''Downloads '''folder.

Double click on the downloaded '''exe''' file.
|-
|| Click '''yes''' on the pop-up message box.
|| Click '''yes''' on the pop-up message asking to give permission to continue the installation.
|-
|| Cursor on''' Choose Install Location '''window.

Click on '''Install''' button at the '''bottom-right '''corner.
|| '''Choose Install Location''' window opens.

You will be prompted to choose a custom location or default location.

The default location would be: C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6.

I will choose the default location and click on '''Install''' button at the bottom-right corner.
|-
|| Close the '''set up '''window.
|| Close the '''set up '''window once you get the message that the installation is completed.
|-
|| Go to the '''C drive Program files''' and ''' locate The Scripps Research Institute '''folder.

Double-click to open the '''Autodock '''folder.

|| After the installation is complete go to the '''C drive Program files(x86)''' and locate '''The Scripps Research Institute '''folder.

Double-click to open the folder, inside this folder you will find the '''Autodock ''' folder.
|-
|| Two executable files '''autodock4.exe '''and''' autogrid4.exe '''are present in the folder.

|| Make sure the two executable files '''autodock4.exe '''and''' autogrid4.exe '''are present in the folder.
|-
|| Cursor on the AutoDock downloads page.
|| Now let us install '''AutoDock Tools'''.
|-
|| Cursor on the AutoDock Downloads page.

Scroll down.
|| Go to the '''autodock downloads''' page which we had opened earlier.

Scroll down to the end of the page.
|-
|| Cursor on the link.
|| You will find the link to download '''AutodockTools''', also referred to as '''ADT'''.
|-
|| Click on the link.

Cursor on the MGL tools page.
|| Click on the link which reads,

'''To download the graphical user interface of AutoDock Tools (ADT), click here'''.

'''MGLTools''' page opens.
|-
|| On the left, click on '''Downloads '''link.

On the '''Downloads''' page,

In the table of available installers for version 1.5.7, Click on the installer file corresponding to Windows OS.

mgltools_win32_1.5.7_Setup.exe (80 Mb)
|| On the left side of the page, click on ''' Downloads''' link.

On the '''Downloads''' page, scroll down.

The table for installers available for version 1.5.7 is seen.

Click on the installer file corresponding to '''Windows''' Operating System.
|-
|| Show the installer file in Downloads folder.

Double-click on the downloaded file.

Click '''yes'''.
|| The installer file downloads to the '''Downloads''' folder.

Double-click on the downloaded file.

Click '''yes''' when prompted to continue with the installation.
|-
|| Click '''Next''' in the MGL Tools Setup window.
|| Click '''Next''' in the MGLTools Setup window.
|-
|| Click the check box to accept the terms of license agreement.

Click on '''Yes''' button.
|| Accept the terms of license agreement in the '''MGL Tools License Agreement''' window.

Click on the '''Yes''' button to continue the installation process.
|-
|| Cursor on the screen.
|| '''Choose Destination Location ''' window opens.

Here, you have an option to accept the default location or '''Browse''' to choose a new location.
|-
|| Click on '''Next''' to continue.
|| I will accept the default location and click on '''Next''' to continue.
|-
|| In the Installing MGL Tools window, click on '''Next'''.
|| In the Installing MGLTools window, click on '''Next'''.
|-
|| In the pop-up window.

Read the message and click on OK.
|| A small pop-up window about commercial usage opens.

Read the message and click on '''OK'''.
|-
|| Check the check boxes for,

Launch PMV

Create Desktop shortcut

Create Quick Launch Shortcut.
|| Installation complete window opens.

I will check the boxes for,

Launch PMV

Create Desktop shortcut

Create Quick Launch Shortcut.
|-
|| Click on the '''Finish '''button to exit the window.
|| Click on the '''Finish '''button to exit the window.
|-
|| Cursor on ADT interface.

Click X at the top of the window.

Cursor on desktop.
|| AutoDock Tools graphical interface opens.

This ensures the successful installation of ADT Tools.

Close the window.

Check for the desktop shortcut for ADT Tools.
|-
|| '''Slide Number 7'''

'''Installation of Autodock 4 and ADT Tools on macOS'''
|| Let us now install '''Autodock 4''' and '''ADT '''Tools on '''macOS '''
|-
|| In Google search type AutoDock download.
|| Open any web browser and search for '''AutoDock download'''.
|-
|| Click on the first link

https://autodock.scripps.edu/download-autodock4/
|| A page opens.

Click on the first link, '''Download Autodock4'''.
|-
|| Click on Autodocsuite-4.2.6-MacOSX.tar
|| On the downloads page, locate the installer file for '''mac. AutoDock4 (Mac OS X)'''

Click on it.
|-
|| Cursor on downloads progress bar.
|| '''Autodocsuite-4.2.6-MacOSX.tar''' file downloads to your '''Downloads''' folder.
|-
|| Go to '''Finder''' and go to the '''Downloads''' folder.

Double-click on the installer file.
|| Go to the '''Downloads''' folder.

Double-click on the installer file.
|-
|| Cursor on '''MacOSX.'''

Double click on '''MacOSX.'''

'''Cursor '''on '''Autodock4''' and '''autogrid4.'''
|| The extracted folder '''MacOSX '''is seen.

Double click to open it.

Here you will see two files, '''Autodock4''' and '''autogrid4.'''
|-
|| '''Slide Number 8'''

'''Installation of XQuartz'''

https://www.xquartz.org/releases/XQuartz-2.8.5.html
|| You may need to install '''XQuartz''' as a prerequisite for '''ADT''' to work on '''mac'''.

Open the given link in any web browser.
|-
|| Under Quick Download heading

Click on the link

'''Xquartz-2.8.5pkg'''
|| On the web page, under '''Installation''' heading,

Click on '''Xquartz-2.8.5pkg '''download link'''.

The file downloads to your '''Downloads '''folder.
|-
|| Show '''Downloads''' folder and double-click on the installer file.

A pop-up window opens , click on '''Continue'''.

Click on the '''Continue '''button on the install window.

Click on''' agree '''in the license agreement window.

Click on '''Continue'''.
|| Go to the '''Downloads''' folder, double-click on the installer file.

A pop-up window opens, click on '''Allow''' button.

In the '''Install''' window, click on the '''Continue '''button at the bottom right corner.

Important information page opens.

Read the information and click on the '''Continue''' button.

Again click the '''Continue '''button on the '''Software License Agreement '''window.

Click on''' Agree '''in the''' software license agreement window.'''

Now click on '''Install button'''.
|-
|| Click on '''Continue installation.'''

Give your system password.
|| A pop-up window asks for your password.

Enter your system password.

Click on the''' Install Software''' button.

The installation begins and the status bar indicates the progress of the installation.
|-
|| Cursor on the message, The '''installation is successful.'''

Click on '''Log Out''' button at the bottom right corner.
|| '''The installation was successful''', message appears.

Click on the '''Close''' button at the bottom right corner.
|-
|| Click on '''Move to Trash''' button.
|| The system prompts you to move the installer to the '''Bin'''.

Click on ''' Move to Bin '''button.

This completes the installation of '''Xquartz'''.
|-
|| Cursor on the AutoDock downloads page.
|| Now let us install '''AutoDock Tools '''on '''macOS.'''
|-
|| Cursor on the AutoDock Downloads page.

Scroll down.
|| Go to the '''autodock''' downloads page which we had opened earlier.

Scroll down to the end of the page.
|-
|| Cursor on the link.
|| You will find the link to download '''AutodockTools''', also referred to as ADT.
|-
|| Click on the link, which reads “To download the graphical user interface of AutoDock Tools (ADT), click here.

Cursor on the MGL tools page.
|| Click on the link. which reads '''To download the graphical user interface of AutoDock Tools (ADT), click here.'''

MGL Tools page opens.
|-
|| On the left side of the page, click on''' Downloads''' link.

On the '''Downloads''' page, scroll down.
|| On the left side of the page, click on''' Downloads''' link.

On the '''Downloads''' page, scroll down.
|-
|| Mgltools-1.5.7-MACOS-X-install.dmg (GUI installer 91 Mb)
|| Scroll down to Version 1.5.7 section and click on the '''dmg''' installer file for mac OS.
|-
|| Cursor on the downloaded installer files.
|| The installer file downloads to your Downloads folder.
|-
|| Doubleclick on the dmg file.

Mgltools-1.5.7-MacOS-X-install.dmg
|| Double click on '''Mgltools-1.5.7-MacOS-X-install''' file.
|-
|| Click on the '''Open''' button.
|| Sometimes a pop window with an error message appears.

In such cases click on '''Cancel''' in the pop-up window.

Go to '''System Settings'''.

Click on '''Privacy and Security.'''

Scroll down the '''Privacy and Security page'''.
|-
|| Go to '''System Preferences'''.

Go to '''Security and Privacy.'''

Cursor on the message.

Click on '''open anyway'''.

In the pop-up window click on '''Open'''.

Exit the '''Security and Privacy''' window.
|| You will see a message at the bottom with '''MGLTools''' listed.

It was blocked from use because it is not from an '''identified developer.'''

Click the '''Open Anyway '''button under the message.

Enter the system password in the pop up window.

Click on '''Modify settings'''.

A new pop up opens. Click on '''Open'''.

Exit the '''Security and Privacy''' window.
|-
|| Click on '''Next '''in MGL Tools install Jammer Wizard.
|| '''MGLTools''' Setup window opens.

In the '''MGLTools''' '''Install Jammer Wizard''' window, click on '''Next'''.
|-
|| Accept the license agreement and click on '''Next'''.
|| In the '''MGLTools''' license agreement page, accept the license agreement and click on '''Next'''.

The Installation process begins.

The status bar indicates the progress of the installation.
|-
|| Click '''Finish'''.
|| Successful installation of '''MGLTools''' message appears.

Click '''Finish''' to exit the wizard.
|-
|| Close the '''Readme '''window.
|| Close the '''Readme '''window.
|-
|| Open the '''Finder''' and go to the '''Applications '''folder.

Cursor on '''MGLTools-1.5.7'''.
|| Go to the '''Applications '''folder.

Locate '''MGLTools-1.5.7'''.
|-
|| Double-click on '''MGLTools-1.5.7 '''folder.
|| Double-click to open the file.

The file opens with various tools .
|-
|| Double-Click on '''AutoDockTools-1.5.7.'''

Cursor on ADT interface.

Close the '''ADT '''interface window.
|| Double-Click on '''AutoDockTools-1.5.7 '''icon to open it.

Click on “'''Remind me later'''” on the bottom right corner of the interface window.

The user interface opens with menus and tools.

We have successfully installed '''ADT''' on our system

This completes the installation of '''AutoDock''' on Mac OS.
|-
|| '''Slide Number 9'''

'''Summary'''
|| Let's summarize.

In this tutorial, we have,

Downloaded and installed '''AutoDock4''' on '''Windows OS'''

Downloaded and installed '''MGLTools'''

Checked the installation of '''AutoDock''' tools.
|-
|| '''Slide Number 10'''

'''Summary'''
|| We have also,

Downloaded and installed '''AutoDock4''' on '''macOS X'''

Downloaded and installed '''XQuartz''' version 2.8.5

|-
|| '''Slide Number 11'''

'''Summary'''
||
Downloaded and installed '''MGLTools'''

Checked the installation of '''AutoDock '''

|-
|| '''Slide''' '''Number 12'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.
|-
|| '''Slide''' '''Number 13'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please contact us.
|-
|| '''Slide Number 14'''

'''Answers for THIS Spoken Tutorial '''
||
* Do you have questions in THIS Spoken Tutorial?
* Please visit this site
* Choose the minute and second where you have the question.
* Explain your question briefly
* The spoken tutorial project will ensure an answer.
* You will have to register on this website to ask questions.
|-
|| '''Slide''' '''Number 15'''

'''Acknowledgement '''
|| Spoken Tutorial project was established by Ministry of Education (MoE), Govt. of India
|-
||
||
* This tutorial is contributed by Snehlatha kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay

Thank you for joining.
|-
|}

AutoDock4/C2/Installation-of-AutoDock4-on-Windows-OS-and-macOS/English

2025-01-24T10:31:46Z

Snehalathak:

'''Title of script''': Installation of AutoDock on Windows and mac

'''Author''': Dr. Snehalatha Kaliappan

'''Keywords''': AutoDock4, AutoDock installation, AutoDock Tools, MGL Tools, Windows OS, macOS, video tutorial.

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Installation of AutoDock4 on Windows OS and macOS'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''AutoDock4''' on '''Windows OS'''

Download and install '''MGLTools'''

Check the installation of '''AutoDockTools '''
|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| We will also,

Download and install '''AutoDock4''' on '''macOS'''

Download and install '''XQuartz''' version 2.8.5

|-
|| '''Slide Number 4'''

'''Learning Objectives''
||
Download and install '''MGLTools'''

Check the installation of '''AutoDockTools''' on '''macOS'''

|-
|| '''Slide Number 5'''

'''System Requirement'''
|| Here I am using

'''Windows 11'''

'''Mac OS''' version 14.5

'''AutoDock''' version 4.2.6

'''MGLTools''' version 1.5.7

'''XQuartz ''' version 2.8.5

'''Firefox ''' web browser version 130.0.1

A working internet connection
|-
|| '''Slide Number 6'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

basic computer operations on '''Windows''' and '''macOS'''
|-
|| Open Firefox web browser.

In the Google search field type, '''AutoDock download''' and press enter.
|| I have opened a google search page in a web browser.

In the Google search field type, '''AutoDock download''' and press Enter.
|-
|| On the google results page,

Click on the first link, '''Download AutoDock4'''

https://autodock.scripps.edu/download-autodock4/
|| A page opens with many results.

Click on the first link, '''Download AutoDock4'''.
|-
|| Cursor on the AutoDock downloads page.
|| This takes you to the '''Autodock download page of Scripps.edu'''.

|-
|| Cursor on the AutoDock downloads page.

[https://autodock.scripps.edu/download-autodock4/ https://autodock.scripps.edu/download-autodock4/]

Click on '''Autodock4 Windows installer file.'''
|| Here, in the center of the page you will see link to installers for various operating systems.

I will click on '''Autodock4 Windows''' installer file.
|-
|| Cursor on the download progress bar at the bottom.
|| '''autodocksuite-4.2.6.i86Windows.exe '''file gets downloaded to your '''Downloads''' folder.
|-
|| Go to the '''Downloads '''folder.

Double click on the downloaded '''autodocksuite-4.2.6.i86Windows.exe '''file.

|| Go to the '''Downloads '''folder.

Double click on the downloaded '''exe''' file.
|-
|| Click '''yes''' on the pop-up message box.
|| Click '''yes''' on the pop-up message asking to give permission to continue the installation.
|-
|| Cursor on''' Choose Install Location '''window.

Click on '''Install''' button at the '''bottom-right '''corner.
|| '''Choose Install Location''' window opens.

You will be prompted to choose a custom location or default location.

The default location would be: C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6.

I will choose the default location and click on '''Install''' button at the bottom-right corner.
|-
|| Close the '''set up '''window.
|| Close the '''set up '''window once you get the message that the installation is completed.
|-
|| Go to the '''C drive Program files''' and ''' locate The Scripps Research Institute '''folder.

Double-click to open the '''Autodock '''folder.

|| After the installation is complete go to the '''C drive Program files(x86)''' and locate '''The Scripps Research Institute '''folder.

Double-click to open the folder, inside this folder you will find the '''Autodock ''' folder.
|-
|| Two executable files '''autodock4.exe '''and''' autogrid4.exe '''are present in the folder.

|| Make sure the two executable files '''autodock4.exe '''and''' autogrid4.exe '''are present in the folder.
|-
|| Cursor on the AutoDock downloads page.
|| Now let us install '''AutoDock Tools'''.
|-
|| Cursor on the AutoDock Downloads page.

Scroll down.
|| Go to the '''autodock downloads''' page which we had opened earlier.

Scroll down to the end of the page.
|-
|| Cursor on the link.
|| You will find the link to download '''AutodockTools''', also referred to as '''ADT'''.
|-
|| Click on the link.

Cursor on the MGL tools page.
|| Click on the link which reads,

'''To download the graphical user interface of AutoDock Tools (ADT), click here'''.

'''MGLTools''' page opens.
|-
|| On the left, click on '''Downloads '''link.

On the '''Downloads''' page,

In the table of available installers for version 1.5.7, Click on the installer file corresponding to Windows OS.

mgltools_win32_1.5.7_Setup.exe (80 Mb)
|| On the left side of the page, click on ''' Downloads''' link.

On the '''Downloads''' page, scroll down.

The table for installers available for version 1.5.7 is seen.

Click on the installer file corresponding to '''Windows''' Operating System.
|-
|| Show the installer file in Downloads folder.

Double-click on the downloaded file.

Click '''yes'''.
|| The installer file downloads to the '''Downloads''' folder.

Double-click on the downloaded file.

Click '''yes''' when prompted to continue with the installation.
|-
|| Click '''Next''' in the MGL Tools Setup window.
|| Click '''Next''' in the MGLTools Setup window.
|-
|| Click the check box to accept the terms of license agreement.

Click on '''Yes''' button.
|| Accept the terms of license agreement in the '''MGL Tools License Agreement''' window.

Click on the '''Yes''' button to continue the installation process.
|-
|| Cursor on the screen.
|| '''Choose Destination Location ''' window opens.

Here, you have an option to accept the default location or '''Browse''' to choose a new location.
|-
|| Click on '''Next''' to continue.
|| I will accept the default location and click on '''Next''' to continue.
|-
|| In the Installing MGL Tools window, click on '''Next'''.
|| In the Installing MGLTools window, click on '''Next'''.
|-
|| In the pop-up window.

Read the message and click on OK.
|| A small pop-up window about commercial usage opens.

Read the message and click on '''OK'''.
|-
|| Check the check boxes for,

Launch PMV

Create Desktop shortcut

Create Quick Launch Shortcut.
|| Installation complete window opens.

I will check the boxes for,

Launch PMV

Create Desktop shortcut

Create Quick Launch Shortcut.
|-
|| Click on the '''Finish '''button to exit the window.
|| Click on the '''Finish '''button to exit the window.
|-
|| Cursor on ADT interface.

Click X at the top of the window.

Cursor on desktop.
|| AutoDock Tools graphical interface opens.

This ensures the successful installation of ADT Tools.

Close the window.

Check for the desktop shortcut for ADT Tools.
|-
|| '''Slide Number 7'''

'''Installation of Autodock 4 and ADT Tools on macOS'''
|| Let us now install '''Autodock 4''' and '''ADT '''Tools on '''macOS '''
|-
|| In Google search type AutoDock download.
|| Open any web browser and search for '''AutoDock download'''.
|-
|| Click on the first link

https://autodock.scripps.edu/download-autodock4/
|| A page opens.

Click on the first link, '''Download Autodock4'''.
|-
|| Click on Autodocsuite-4.2.6-MacOSX.tar
|| On the downloads page, locate the installer file for '''mac. AutoDock4 (Mac OS X)'''

Click on it.
|-
|| Cursor on downloads progress bar.
|| '''Autodocsuite-4.2.6-MacOSX.tar''' file downloads to your '''Downloads''' folder.
|-
|| Go to '''Finder''' and go to the '''Downloads''' folder.

Double-click on the installer file.
|| Go to the '''Downloads''' folder.

Double-click on the installer file.
|-
|| Cursor on '''MacOSX.'''

Double click on '''MacOSX.'''

'''Cursor '''on '''Autodock4''' and '''autogrid4.'''
|| The extracted folder '''MacOSX '''is seen.

Double click to open it.

Here you will see two files, '''Autodock4''' and '''autogrid4.'''
|-
|| '''Slide Number 8'''

'''Installation of XQuartz'''

https://www.xquartz.org/releases/XQuartz-2.8.5.html
|| You may need to install '''XQuartz''' as a prerequisite for '''ADT''' to work on '''mac'''.

Open the given link in any web browser.
|-
|| Under Quick Download heading

Click on the link

'''Xquartz-2.8.5pkg'''
|| On the web page, under '''Installation''' heading,

Click on '''Xquartz-2.8.5pkg '''download link'''.

The file downloads to your '''Downloads '''folder.
|-
|| Show '''Downloads''' folder and double-click on the installer file.

A pop-up window opens , click on '''Continue'''.

Click on the '''Continue '''button on the install window.

Click on''' agree '''in the license agreement window.

Click on '''Continue'''.
|| Go to the '''Downloads''' folder, double-click on the installer file.

A pop-up window opens, click on '''Allow''' button.

In the '''Install''' window, click on the '''Continue '''button at the bottom right corner.

Important information page opens.

Read the information and click on the '''Continue''' button.

Again click the '''Continue '''button on the '''Software License Agreement '''window.

Click on''' Agree '''in the''' software license agreement window.'''

Now click on '''Install button'''.
|-
|| Click on '''Continue installation.'''

Give your system password.
|| A pop-up window asks for your password.

Enter your system password.

Click on the''' Install Software''' button.

The installation begins and the status bar indicates the progress of the installation.
|-
|| Cursor on the message, The '''installation is successful.'''

Click on '''Log Out''' button at the bottom right corner.
|| '''The installation was successful''', message appears.

Click on the '''Close''' button at the bottom right corner.
|-
|| Click on '''Move to Trash''' button.
|| The system prompts you to move the installer to the '''Bin'''.

Click on ''' Move to Bin '''button.

This completes the installation of '''Xquartz'''.
|-
|| Cursor on the AutoDock downloads page.
|| Now let us install '''AutoDock Tools '''on '''macOS.'''
|-
|| Cursor on the AutoDock Downloads page.

Scroll down.
|| Go to the '''autodock''' downloads page which we had opened earlier.

Scroll down to the end of the page.
|-
|| Cursor on the link.
|| You will find the link to download '''Autodock Tools''', also referred to as ADT.
|-
|| Click on the link, which reads “To download the graphical user interface of AutoDock Tools (ADT), click here.

Cursor on the MGL tools page.
|| Click on the link. which reads '''To download the graphical user interface of AutoDock Tools (ADT), click here.'''

MGL Tools page opens.
|-
|| On the left side of the page, click on''' Downloads''' link.

On the '''Downloads''' page, scroll down.
|| On the left side of the page, click on''' Downloads''' link.

On the '''Downloads''' page, scroll down.
|-
|| Mgltools-1.5.7-MACOS-X-install.dmg (GUI installer 91 Mb)
|| Scroll down to Version 1.5.7 section and click on the '''dmg''' installer file for mac OS.
|-
|| Cursor on the downloaded installer files.
|| The installer file downloads to your Downloads folder.
|-
|| Doubleclick on the dmg file.

Mgltools-1.5.7-MacOS-X-install.dmg
|| Double click on Mgltools-1.5.7-MacOS-X-install file.
|-
|| Click on the '''Open''' button.
|| Sometimes a pop window with an error message appears.

In such cases click on '''Cancel''' in the pop-up window.

Go to '''System Settings'''.

Click on '''Privacy and Security.'''

Scroll down the '''Privacy and Security page'''.
|-
|| Go to '''System Preferences'''.

Go to '''Security and Privacy.'''

Cursor on the message.

Click on '''open anyway'''.

In the pop-up window click on '''Open'''.

Exit the '''Security and Privacy''' window.
|| You will see a message at the bottom with '''MGLTools''' listed.

It was blocked from use because it is not from an '''identified developer.'''

Click the '''Open Anyway '''button under the message.

Enter the system password in the pop up window.

Click on '''Modify settings'''.

A new pop up opens. Click on '''Open'''.

Exit the '''Security and Privacy''' window.
|-
|| Click on '''Next '''in MGL Tools install Jammer Wizard.
|| '''MGLTools''' Setup window opens.

In the '''MGLTools''' '''Install Jammer Wizard''' window, click on '''Next'''.
|-
|| Accept the license agreement and click on '''Next'''.
|| In the '''MGLTools''' license agreement page, accept the license agreement and click on '''Next'''.

The Installation process begins.

The status bar indicates the progress of the installation.
|-
|| Click '''Finish'''.
|| Successful installation of '''MGLTools''' message appears.

Click '''Finish''' to exit the wizard.
|-
|| Close the '''Readme '''window.
|| Close the '''Readme '''window.
|-
|| Open the '''Finder''' and go to the '''Applications '''folder.

Cursor on '''MGLTools-1.5.7'''.
|| Go to the '''Applications '''folder.

Locate '''MGLTools-1.5.7'''.
|-
|| Double-click on '''MGLTools-1.5.7 '''folder.
|| Double-click to open the file.

The file opens with various tools .
|-
|| Double-Click on '''AutoDockTools-1.5.7.'''

Cursor on ADT interface.

Close the '''ADT '''interface window.
|| Double-Click on '''AutoDockTools-1.5.7 '''icon to open it.

Click on “'''Remind me later'''” on the bottom right corner of the interface window.

The user interface opens with menus and tools.

We have successfully installed '''ADT''' on our system

This completes the installation of '''AutoDock''' on Mac OS.
|-
|| '''Slide Number 9'''

'''Summary'''
|| Let's summarize.

In this tutorial, we have,

Downloaded and installed '''AutoDock4''' on '''Windows OS'''

Downloaded and installed '''MGLTools'''

Checked the installation of '''AutoDock''' tools.
|-
|| '''Slide Number 10'''

'''Summary'''
|| We have also,

Downloaded and installed '''AutoDock4''' on '''macOS X'''

Downloaded and installed '''XQuartz''' version 2.8.5

|-
|| '''Slide Number 11'''

'''Summary'''
||
Downloaded and installed '''MGLTools'''

Checked the installation of '''AutoDock '''

|-
|| '''Slide''' '''Number 12'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.
|-
|| '''Slide''' '''Number 13'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please contact us.
|-
|| '''Slide Number 14'''

'''Answers for THIS Spoken Tutorial '''
||
* Do you have questions in THIS Spoken Tutorial?
* Please visit this site
* Choose the minute and second where you have the question.
* Explain your question briefly
* The spoken tutorial project will ensure an answer.
* You will have to register on this website to ask questions.
|-
|| '''Slide''' '''Number 15'''

'''Acknowledgement '''
|| Spoken Tutorial project was established by Ministry of Education (MoE), Govt. of India
|-
||
||
* This tutorial is contributed by Snehlatha kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay

Thank you for joining.
|-
|}

AutoDock4/C2/Installation-of-AutoDock4-on-Windows-OS-and-macOS/English

2025-01-17T11:36:06Z

Snehalathak: Created page with " {|border=1 |- || Visual Cue || Narration |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this tutorial on Installation of AutoDock4 on Windows and mac. |- ||..."

{|border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on Installation of AutoDock4 on Windows and mac.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

Download and install '''AutoDock4''' on '''Windows OS'''

Download and install '''MGLTools'''

Check the installation of '''AutoDockTools '''
|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| We will also,

Download and install '''AutoDock4''' on '''macOS '''

Download and install '''XQuartz''' version 2.8.5

Download and install '''MGLTools'''

Check the installation of '''AutoDockTools''' on '''macOS'''
|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using

'''Windows 11'''

'''Mac OS''' version 14.5

'''AutoDock''' version 4.2.6

'''MGLTools''' version 1.5.7

'''XQuartz '''version 2.8.5

'''Firefox '''web browser version 130.0.1

A working internet connection
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial you should be familiar with,

basic computer operations on '''Windows''' and '''macOS'''
|-
|| Open Firefox web browser.

In the Google search field type, AutoDock download and press enter.
|| I have opened a google search page in a web browser.

In the Google search field type, '''AutoDock download''' and press enter.
|-
|| On the google results page,

Click on the first link, '''Download AutoDock4'''

https://autodock.scripps.edu/download-autodock4/
|| A page opens with many results.

Click on the first link, '''Download AutoDock4. '''
|-
|| Cursor on the AutoDock downloads page.
|| This takes you to the autodock download page of Scripps.edu.
|-
|| Cursor on the AutoDock downloads page.

[https://autodock.scripps.edu/download-autodock4/ https://autodock.scripps.edu/download-autodock4/]

Click on '''Autodock4 Windows installer file.'''
|| Here, in the center of the page you will see a link to installers for various OS.

I will click on '''Autodock4 Windows''' installer file.
|-
|| Cursor on the download progress bar at the bottom.
|| '''autodocksuite-4.2.6.i86Windows.exe '''file gets downloaded to your downloads folder.
|-
|| Go to the '''Downloads '''folder. Double click on the downloaded '''autodocksuite-4.2.6.i86Windows.exe '''file.
|| Go to the '''Downloads '''folder. Double click on the downloaded '''exe''' file.
|-
|| Click '''yes''' on the pop-up message box.
|| Click '''yes''' on the pop-up message asking to give permission to continue the installation.
|-
|| Cursor on''' Choose Install Location '''window.

Click on '''Install''' button at the '''bottom-right '''corner.
|| '''Choose Install Location''' window opens.

You will be prompted to choose a custom location or default location.

The default location would be : C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6.

I will choose the default location and click on '''Install''' button at the '''bottom-right '''corner.
|-
|| Close the '''set up '''window.
|| Close the '''set up '''window once you get the message that the installation is completed.
|-
|| Go to the C drive Program files and''' locate The Scripps Research Institute '''folder.

Double-click to open the '''Autodock '''folder.
|| After the installation is complete go to the C drive Program files(x86) and''' locate The Scripps Research Institute '''folder.

Double-click to open the folder, inside this folder you will find the '''Autodock '''folder.
|-
|| Two executable files '''autodock4.exe '''and''' autogrid4.exe '''are present in the folder.
|| Make sure the two executable files '''autodock4.exe '''and''' autogrid4.exe '''are present in the folder.
|-
|| Cursor on the AutoDock downloads page.
|| Now let us install '''AutoDock Tools.'''
|-
|| Cursor on the AutoDock Downloads page.

Scroll down.
|| Go to the '''autodock downloads''' page which we had opened earlier.

Scroll down to the end of the page.
|-
|| Cursor on the link.
|| You will find the link to download '''AutodockTools''', also referred to as '''ADT'''.
|-
|| Click on the link.

Cursor on the MGL tools page.
|| Click on the link. which reads,

'''To download the graphical user interface of AutoDock Tools (ADT), click here.'''

'''MGLTools''' page opens.
|-
|| On the left, click on '''Downloads '''link.

On the '''Downloads''' page,

In the table of available installers for version 1.5.7, Click on the installer file corresponding to Windows OS.

mgltools_win32_1.5.7_Setup.exe (80 Mb)
|| On the left side of the page, click on''' Downloads''' link.

On the '''Downloads''' page, scroll down.

The table for installers available for version 1.5.7 is seen.

Click on the installer file corresponding to '''Windows''' Operating System.
|-
|| Show the installer file in Downloads folder.

Double-click on the downloaded file.

Click '''yes'''.
|| The installer file downloads to the '''Downloads''' folder.

Double-click on the downloaded file.

Click '''yes''' when prompted to continue with the installation.
|-
|| Click '''Next''' in the MGL Tools Setup window.
|| Click '''Next''' in the MGLTools Setup window.
|-
|| Click the check box to accept the terms of license agreement.

Click on '''Yes''' button.
|| Accept the terms of license agreement in the '''MGL Tools License Agreement''' window.

Click on the '''Yes''' button to continue the installation process.
|-
|| Cursor on the screen.
|| '''Choose Destination Location '''window opens.

Here, you have an option to accept the default location or '''Browse''' to choose a new location.
|-
|| Click on '''Next''' to continue.
|| I will accept the default location and click on '''Next''' to continue.
|-
|| In the Installing MGL Tools window, click on '''Next'''
|| In the Installing MGLTools window, click on '''Next.'''
|-
|| In the pop-up window.

Read the message and click on OK.
|| A small pop-up window about commercial usage opens.

Read the message and click on '''OK'''.
|-
|| Check the check boxes for,

Launch PMV

Create Desktop shortcut

Create Quick Launch Shortcut.
|| Installation complete window opens.

I will check the checkboxes for,

Launch PMV

Create Desktop shortcut

Create Quick Launch Shortcut.
|-
|| Click on the '''Finish '''button to exit the window.
|| Click on the '''Finish '''button to exit the window.
|-
|| Cursor on ADT interface.

Click X at the top of the window.

Cursor on desktop.
|| AutoDock Tools graphical interface opens. This ensures the successful installation of ADT Tools.

Close the window.

Check for the desktop shortcut for ADT Tools.
|-
|| '''Slide Number 6'''

'''Installation of Autodock 4 and ADT Tools on macOS'''
|| Let us now install '''Autodock 4''' and '''ADT '''Tools on '''macOS '''
|-
|| In Google search type AutoDock download.
|| Open any web browser and search for AutoDock download.
|-
|| Click on the first link

https://autodock.scripps.edu/download-autodock4/
|| A page opens.

Click on the first link, Download Autodock4.
|-
|| Click on Autodocsuite-4.2.6-MacOSX.tar
|| On the downloads page, locate the installer file for mac. AutoDock4 (Mac OS X)

Click on it.
|-
|| Cursor on downloads progress bar.
|| '''Autodocsuite-4.2.6-MacOSX.tar''' file downloads to your Downloads folder.
|-
|| Go to '''Finder''' and go to the '''Downloads''' folder. Double-click on the installer file.
|| Go to the '''Downloads''' folder. Double-click on the installer file.
|-
|| Cursor on '''MacOSX.'''

Double click on '''MacOSX.'''

'''Cursor '''on '''Autodock4''' and '''autogrid4.'''
|| The extracted folder '''MacOSX '''is seen.

Double click to open it.

Here you will see two files. '''Autodock4''' and '''autogrid4.'''
|-
|| '''Slide Number 7'''

'''Installation of XQuartz'''

https://www.xquartz.org/releases/XQuartz-2.8.5.html
|| You may need to install '''XQuartz''' as a prerequisite for '''ADT''' to work on '''mac'''.

Open the given link in any web browser.
|-
|| Under Quick Download heading

Click on the link

'''Xquartz-2.8.5pkg'''
|| On the web page, under '''Installation''' heading,

Click on '''Xquartz-2.8.5pkg '''download link'''.'''

The file downloads to your '''Downloads '''folder.
|-
|| Show '''Downloads''' folder and double-click on the installer file.

A pop-up window opens , click on '''Continue'''.

Click on the '''Continue '''button on the install window.

Click on''' agree '''in the license agreement window.

Click on '''Continue'''.
|| Go to the '''Downloads''' folder, double-click on the installer file.

A pop-up window opens, click on '''Allow''' button.

In the '''Install''' window, click on the '''Continue '''button at the bottom right corner.

Important information page opens. Read the information and click on the '''Continue''' button.

Again click the '''Continue '''button on the '''Software License Agreement '''window.

Click on''' Agree '''in the''' software licence agreement window.'''

Now Click on '''Install button'''.
|-
|| Click on '''Continue installation.'''

Give your system password.
|| A pop-up window asks for your password.

Enter your system password.

Click on the''' Install Software''' button.

The installation begins and the status bar indicates the progress of the installation.
|-
|| Cursor on the message, The '''installation is successful.'''

Click on '''Log Out''' button at the bottom right corner.
|| '''The''' i'''nstallation was successful. '''message appears.

Click on the '''Close''' button at the bottom right corner.
|-
|| Click on '''Move to Trash''' button.
|| The system prompts you to move the installer to the '''Bin.''' Click on''' Move to Bin '''button.

This completes the installation of '''Xquartz'''.
|-
|| Cursor on the AutoDock downloads page.
|| Now let us install '''AutoDock Tools '''on '''macOS.'''
|-
|| Cursor on the AutoDock Downloads page.

Scroll down.
|| Go to the '''autodock''' downloads page which we had opened earlier.

Scroll down to the end of the page.
|-
|| Cursor on the link.
|| You will find the link to download '''Autodock Tools''', also referred to as ADT.
|-
|| Click on the link, which reads “To download the graphical user interface of AutoDock Tools (ADT), click here.

Cursor on the MGL tools page.
|| Click on the link. which reads '''To download the graphical user interface of AutoDock Tools (ADT), click here.'''

MGL Tools page opens.
|-
|| On the left side of the page, click on''' Downloads''' link.

On the '''Downloads''' page, scroll down.
|| On the left side of the page, click on''' Downloads''' link.

On the '''Downloads''' page, scroll down.
|-
|| Mgltools-1.5.7-MACOS-X-install.dmg (GUI installer 91 Mb)
|| Scroll down to Version 1.5.7 section and click on the dmg installer file for mac OS.
|-
|| Cursor on the downloaded installer files.
|| The installer file downloads to your Downloads folder.
|-
|| Doubleclick on the dmg file.

Mgltools-1.5.7-MacOS-X-install.dmg
|| Double click on Mgltools-1.5.7-MacOS-X-install file.
|-
|| Click on the '''Open''' button.
|| Sometimes a pop window with an error message appears.

In such cases click on '''Cancel''' in the pop-up window.

Go to '''System Settings'''.

Click on '''Privacy and Security.'''

Scroll down the '''Privacy and Security page.'''
|-
|| Go to '''System Preferences'''.

Go to '''Security and Privacy.'''

Cursor on the message.

Click on '''open anyway'''.

In the pop-up window click on '''Open'''.

Exit the '''Security and Privacy''' window.
|| You will see a message at the bottom with '''MGLTools''' listed.

It was blocked from use because it is not from an '''identified developer.'''

Click the '''Open Anyway '''button under the message.

Enter the system password in the pop up window.

Click on '''Modify settings'''.

A new pop up opens. Click on '''Open. '''

Exit the '''Security and Privacy''' window.
|-
|| Click on '''Next '''in MGL Tools install Jammer Wizard.
|| '''MGLTools''' Setup window opens.

In the '''MGLTools''' '''Install Jammer Wizard''' window, click on '''Next.'''
|-
|| Accept the license agreement and click on '''Next'''.
|| In the '''MGLTools''' license agreement page, accept the license agreement and click on '''Next'''.

The Installation process begins.

The status bar indicates the progress of the installation.
|-
|| Click '''Finish'''.
|| Successful installation of '''MGLTools''' message appears.

Click '''Finish''' to exit the wizard.
|-
|| Close the '''Readme '''window.
|| Close the '''Readme '''window.
|-
|| Open the '''Finder''' and go to the '''Applications '''folder.

Cursor on '''MGLTools-1.5.7'''.
|| Go to the '''Applications '''folder.

Locate '''MGLTools-1.5.7'''.
|-
|| Double-click on '''MGLTools-1.5.7 '''folder.
|| Double-click to open the file.

The file opens with various tools .
|-
|| Double-Click on '''AutoDockTools-1.5.7.'''

Cursor on ADT interface.

Close the '''ADT '''interface window.
|| Double-Click on '''AutoDockTools-1.5.7 '''icon to open it.

Click on “'''Remind me later'''” on the bottom right corner of the interface window.

The user interface opens with menus and tools.

We have successfully installed '''ADT''' on our system

This completes the installation of '''AutoDock''' on Mac OS.
|-
|| '''Slide Number 8'''

'''Summary'''
|| Let's summarize.

In this tutorial, we have,

Downloaded and installed '''AutoDock4''' on '''Windows OS'''

Downloaded and installed '''MGLTools'''

Checked the installation of '''AutoDock'''
|-
|| '''Slide Number 9'''

'''Summary'''
|| We have also,

Downloaded and installed '''AutoDock4''' on '''macOS X'''

Downloaded and installed '''XQuartz''' version 2.8.5

Downloaded and installed '''MGLTools'''

Checked the installation of '''AutoDock '''
|-
|| '''Slide''' '''Number 10'''

'''About Spoken Tutorial Project '''
|| * The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.
|-
|| '''Slide''' '''Number 11'''

'''Spoken tutorial workshops '''
|| * We conduct workshops using spoken tutorials and give certificates.
* For more details, please contact us.
|-
|| '''Slide Number 12'''

'''Answers for THIS Spoken Tutorial '''
|| * Do you have questions in THIS Spoken Tutorial?
* Please visit this site
* Choose the minute and second where you have the question.
* Explain your question briefly
* The spoken tutorial project will ensure an answer.
* You will have to register on this website to ask questions.
|-
|| '''Slide''' '''Number 14'''

'''Acknowledgement '''
|| Spoken Tutorial project was established by Ministry of Education (MoE), Govt. of India
|-
||
|| * This tutorial is contributed by Snehlatha kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay

Thank you for joining.
|-
|}

Blender-4.1/C3/Modeling-Car-Parts/English

2024-11-13T10:00:00Z

Snehalathak:

'''Title: '''Modeling Car Parts

'''Author: '''Sejal Dhiman and Arthi Varadarajan

'''Keywords: '''blender 4.1, car accessories, modeling, wheel, headlight, backlight, video tutorial.

{|border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the Spoken tutorial on '''Modeling Car Parts '''in '''Blender 4.1'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to model,
* Car wheel
* Headlights and backlights and
* Radiator
|-
|| '''Slide Number 3'''

'''System Requirements'''
|| To record this tutorial, I am using
* '''Mac OS version '''14.5
* '''Blender version''' 4.1

It is recommended to install '''Blender version ''' 4.1 or higher.
|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org]
|| To follow this tutorial,
* The learner must be familiar with editing objects in '''Blender'''.

* Please access the relevant tutorials on this website.
|-
|| Show Car.blend file
|| Let us open the '''Car.blend''' file which we had created earlier.
|-
|| Select '''Car.blend >> Open'''

Point to the car
|| Locate the '''Car-animation '''folder.

Select '''Car.blend '''and ''' Open'''.

Now, we will start adding parts to our car.

|-
|| Video Editor: '''numpad 3'''

Video Editor: '''Z'''

Press '''Shift''' and Right click
|| We shall start modeling the wheels of the car with the help of a '''Cylinder'''.

Press '''numpad 3''' to go to '''Side view'''.

Press '''Z''' and select '''Wireframe''' from the shown options.

Press '''Shift''' key and right click in the center of the front wheel space.

The '''3D cursor''' is now shifted here.
|-
|| '''Add menu >> Mesh >> Cylinder'''
|| Go to '''Add menu'''.

Select '''Mesh''' and click on '''Cylinder'''.
|-
|| '''Add cylinder >> '''Set the''' Vertices''' to '''24'''

'''Rotation '''>> '''Y '''value to''' 90'''
|| Click on the '''Add cylinder''' option.

Set the '''Vertices''' to 24.

In ''' Rotation '''set the ''' Y ''' value to 90.

Press ''' Enter'''.
|-
|| '''Properties >> Object'''

'''Scale >> X''' & '''Y''' value to 0.05, '''Z''' to 0.2 >> Press '''Enter'''.

Video Editor: '''G'''
|| Go to '''Properties'''.

Select '''Object properties'''.

In the '''Scale''' option, set '''X ''' and ''' Y '''values to 0.5 and '''Z '''value to 0.2.

Press '''Enter'''.

Press '''G''' and move the cylinder to the center portion of the wheel space.

Three fourths of the cylinder should be inside the car.
|-
|| Video Editor: '''numpad 7'''

Video Editor: '''G'''

Video Editor: '''X'''
|| Press '''numpad 7''' to go to '''Top view'''.

Press '''G''' and '''X '''and move the cylinder inside the wheel space.
|-
|| Go to '''User perspective mode'''

Video Editor: '''Z'''

Select''' Solid'''

Video Editor: '''Tab'''
|| Hold the mouse wheel and move the mouse to go to '''User perspective view'''.

Press '''Z''' and select '''Solid ''' from the shown options.

Press '''Tab''' to go to'''Edit mode'''.
|-
|| '''Inset faces >> '''set the '''Thickness''' to 0.3
|| Select the front face.

Press '''I''' to '''Inset''' the '''face''' and move the mouse and click.

In the '''Inset faces,''' set the '''Thickness''' to 0.3.

Press '''Enter.'''
|-
|| Video Editor: '''E'''

Point to''' Extrude Region and Move'''.

Change Z value to -0.1.
|| Press '''E''' and extrude the face a little bit inside.

In the '''Extrude Region '''option, change the '''Z''' value to -0.1.

Press '''Enter'''.

Repeat this process twice to create 2 more similar rings.
|-
|| Video Editor: '''S'''

'''Resize >> '''set all values to '''0.5'''

'''Extrude region >> Z''' value 0.2

Video Editor: '''E'''
|| Press '''S''' and scale down the face.

In the '''Resize''' option, set all the values to 0.5.

Press '''Enter'''.

Press '''E''' to extrude the face outside.

In the '''Extrude Region''', set the '''Z''' value to 0.2.

Press '''Enter'''.
|-
|| Video Editor: '''Alt'''
|| Select any '''face''' of the inside ring as shown.

Now hold the '''Alt''' key and click on the next face.

This will select other faces of the ring.
|-
|| '''3D viewport menu >> Select menu >> Checker deselect'''
|| Go to the '''3D viewport menu'''.

Click on the '''Select menu'''.

From the submenu, select '''Checker deselect'''.

This option selects the alternate''' faces'''.
|-
|| Video Editor: '''Alt '''and '''E'''
|| Press '''Alt '''and''' E''' keys together.

Click on '''Extrude Faces along Normals''' from the shown menu.

Bring the faces towards the front, inside the front drum and click.
|-
|| Video Editor: '''Tab'''
|| Press '''Tab''' to go to '''Object mode.

The front wheel is created.
|-
|| Only narration
|| We can add the other wheels after animating the car in the upcoming tutorials.
|-
|| Video Editor: '''numpad 1'''

Press '''Shift''' + Right click
|| Next we will create headlights for the car.

Press '''numpad 1''' to move to the front view of the car.

Press '''Shift''' and right click in the front side right corner as shown.

The '''3D cursor''' is now shifted here.
|-
|| '''Add menu>> Mesh >> UV Sphere'''
|| Go to the '''Add menu. '''Select '''Mesh''' and click on '''UV Sphere.'''
|-
|| '''Add UV Sphere >> '''set the''' Segments '''to 12

'''Properties >> Object'''

'''Scale >> X '''to 0.3, '''Y''' to 0.2, '''Y''' to 0.3
|| In the bottom, in the '''Add UV Sphere''', set the '''segments''' to 12.

Press '''Enter.'''

Go to '''Properties. '''Select '''Object'''.

Change the '''X''' value of '''Scale''' to 0.3, '''Y''' to 0.2 and '''Z''' value to 0.3.

Press '''Enter'''.
|-
|| Hover on the light
|| Now the light is created.

Now let us duplicate this for the left side of the car.
|-
|| Video Editor: '''Shift''' and '''D'''

Video Editor: '''G'''

Video Editor: '''X'''
|| Press '''Shift''' and '''D''' keys together.

Press '''G''' and''' X '''.

Move the duplicated headlight to the left side of the car as shown.
|-
|| Video Editor: '''numpad 7'''
|| Similarly we will duplicate these for the backlights of the car.

Press '''numpad 7''' to go to '''Top view'''.

Hold the '''Shift''' key and select both the headlights.
|-
|| Video Editor: '''Shift''' and '''D'''
|| Press '''Shift''' and '''D''' keys together to duplicate the lights.
|-
|| Video Editor: '''G'''

Video Editor: '''Y'''
|| Press '''G''' and '''Y''' and move the duplicated lights to the backside of the car.
|-
|| Point to the lights
|| Check the position of the lights.
|-
|| Video Editor: '''numpad 1'''

Press '''Shift '''and right click
|| Next we shall model the radiator of the car using a cube.

Press '''numpad 1''' to go to the '''Front view''' of the car.

Press '''Shift '''and right click on the center of the car to shift the '''3D cursor'''.
|-
|| '''Add menu >> Mesh >> Cube'''
|| Go to the '''Add menu'''.

Select '''Mesh''' and click on '''Cube'''.

Next we shall resize this cube.
|-
|| '''Properties >> Object'''

'''Scale >> X''' value to 1.2, '''Y''' to 0.2 & '''Z''' to -0.2

Video Editor: '''G'''
|| Click on '''Object Properties. '''

In the '''Scale''' option, change the '''X''' value to 1.2, '''Y''' to 0.2 and '''Z''' to -0.2. Press '''Enter'''.

Press '''G''' and move the object in the center of the 2 headlights.
|-
|| Video Editor: '''numpad 7'''

Video Editor: '''G'''

Video Editor: '''Y'''
|| Press '''numpad 7''' to go '''Top view'''.

Press '''G''' and '''Y''' and move the object inside as shown.

Maximum portion of the object should be inside the car.
|-
|| Video Editor: '''numpad 1'''

Video Editor: '''Tab'''

Video Editor: '''Ctrl''' and '''R'''
|| Let us edit the object to make it look like a radiator.

Press '''numpad 1''' to go '''Front view'''.

Press '''Tab''' to go to '''Edit mode'''.

Move the mouse onto the object.

Press '''Ctrl''' and '''R''' keys together to show the '''Loop cut '''.
|-
|| Add '''loop cut''' horizontally

'''Loop cut and Slides>> Number of Cuts''' to 10.
|| Double click to add the '''loop cut''' horizontally.

In the '''Loop cut and Slides''' option, change the '''Number of Cuts''' to 10.

Press '''Enter'''.
|-
|| '''3D viewport menu >> Face selection mode'''

Select the alternate '''faces'''

Video Editor: '''Alt''' and '''E'''
|| Click on '''Face selection mode'''.

Press '''Shift''' and select the alternate '''faces''' as shown.

Go to '''User perspective view. '''

Press '''E''' and move the mouse and push the faces inwards and click.
|-
|| '''Extrude region >> Z''' value to -0.03

Video Editor: '''Tab'''
|| In the '''Extrude region''', change the '''Z''' value to -0.03.

Press '''Enter'''.

Press '''Tab''' to go to '''Object mode'''.

The radiator is now created.
|-
|| Video editor: '''Ctrl''' and '''S'''
|| Press '''Ctrl''' and '''S '''keys together to save the file.

With this we have come to the end of this tutorial.
|-
|| '''Slide Number 5'''

'''Summary'''
|| Let us summarize.

In this tutorial, we learnt to model
* Car wheel
* Headlights and backlights and
* Radiator
|-
|| '''Slide number 6'''

'''Assignment'''
|| As an assignment, please do the following:

Add different parts to the jeep model which you made earlier.

After adding the jeep parts the jeep should look like this.
|-
|| '''Slide number 7'''

'''About the Spoken Tutorial Project'''
|| The video at the following link summarizes the '''Spoken Tutorial project.'''

Please download and watch it.
|-
|| '''Slide number 8'''

'''Spoken Tutorial workshops'''
|| The '''Spoken Tutorial Project''' team conducts workshops and gives certificates.

For more details, please write to us.
|-
|| '''Slide number 9'''

'''Answers for THIS Spoken Tutorial'''
|| Please post your timed queries in this '''forum'''.
|-
|| '''Slide number 10'''

'''FOSSEE Forum'''
|| For any general or technical questions on '''Blender''', visit the '''FOSSEE''' '''forum''' and post your question.
|-
|| '''Slide number 11'''

'''Acknowledgement'''
|| '''The Spoken Tutorial''' project was established by the '''Ministry of Education''', '''Government of India'''.
|-
||
|| This is Arthi along with Sejal from '''IIT Bombay''' signing off.

Thanks for joining.
|-
|}

AutoDock4

2024-10-04T12:07:52Z

Snehalathak: Created page with " '''AutoDock4''' AutoDock is a molecular modeling simulation software. It is specifically used for protein-ligand docking. AutoDock consists of a suite of automated docki..."

'''AutoDock4'''

AutoDock is a molecular modeling simulation software. It is specifically used for protein-ligand docking. AutoDock consists of a suite of automated docking tools. They are designed to predict how small molecules, such as substrates or drug candidates bind to a receptor of known 3D structure. In addition to using them for docking, the atomic affinity grids can also be visualized. This can help synthetic organic chemists design better binders. Autodock4 is a computational docking program based on an empirical free energy force field and rapid Lamarckian genetic algorithm search method.

The Spoken Tutorial Effort for AutoDock4 has being contributed by Dr. Snehalatha Kaliappan and Ms. Madhuri Ganapathi with domain reviews done by Ms. Sruthi Sudhakar, Chemistry Dept, IIT Bombay.

'''Learners''': Undergraduate and post-graduate students, research scholars in the fields of Chemistry, Biochemistry, Molecular Biology, Bioinformatics.

Drug-discovery experts, Pharmaceutical company scientists.

__TOC__

==Basic Level==

'''1. Installation of AutoDock4 on Linux OS '''

* Visit AutoDock website.
* Download AutoDock suite 4.2.6 installer file for Linux OS.
* Visit MGL tools web page.
* About MGL tools.
* Download MGL tools 1.5.7 installer file.
* Download User Manual and Examples PDF file.
* Installation of AutoDock on Linux 20.04 OS.
* Installation of MGL tools.
* Open the README file and check the instructions for creating aliases.
* Open bashrc file and change the path for the location of mgl tools files.
* Create aliases for using ADT and PMV.
* Open the GUI for ADT and PMV.

'''2. Getting Started with Docking'''

* Visit RCSB Protein Data Bank website.
* Download ligand and protein files from the RCSB database.
* Move the downloaded files to home folder.
* Open ADT interface using the terminal.
* Perform ligand refinement using AutoDockTools.
* Add hydrogens to the ligand structure.
* Save the structure as PDB file.
* Display root atom.
* Display allowed torsions in the ligand structure
* Save the refined ligand as pdbqt file.

'''3. Receptor Preparation for Docking'''

* Open the ADT GUI.
* Open the receptor pdb file on the ADT display panel.
* Delete the water molecules from the receptor structure.
* Add hydrogens to the receptor structure.
* Remove the ligand molecule crystallized along with the receptor.
* Save the current session.

'''4. Running AutoGrid '''

* Open the saved .psf session file in ADT.
* Save the receptor file as pdbqt file.
* About the grid box.
* Set the grid box parameters.
* Create a grid for the receptor molecule.
* Save the grid box properties as .gpf file.
* Run the AutoGrid program.
* Open the output .glg file using text editor.
* Check the output .glg file for the successful running of the AutoGrid program.

'''5. Running AutoDock'''

* Open the PDBQT files for receptor and ligand for docking on ADT interface.
* Perform docking run using default docking parameters.
* Save the output as .dpf file.
* Set docking parameters.
* Run AutoDock.
* Open the .dlg file to make sure the autodock run is successfully completed.

'''6. Analyzing Docking Runs'''

* Open dlg file on the ADT panel.
* Open and visualize conformations of ligand on ADT panel.
* Analyze the binding energies of various conformations.
* Change the display of ligand to sticks
* Change the color of atoms in ligand.
* Change the display of receptor to cartoon.
* Change the color of residues in the receptor.
* Analyze clusters of conformations.
* Open dlg file with a text editor and analyze the data.
* Export the most favorable docking pose as pdb file.

'''7. Visualyzing Docking using UCSF Chimera'''

* Open the PDB file for the receptor on the Chimera interface.
* Select and delete, ligand, water and glycerol molecules from the receptor structure.
* Add the most preferred docking pose of ligand to the receptor structure.
* Show hydrogen bonds and change the color of the bonds.
* Show hydrogen bond length and energy.
* Show non-bonding interactions and change the color of the pseudo-bonds.
* Highlight the active site residues, change their display format and color.
* Show the surface for the receptor-ligand complex colored by the amino acid hydrophobicity.
* Show the interior of the binding pocket using the Viewing Controls in the tools menu on Chimera interface.

Blender-4.1/C3/Modeling-a-Car/English

2024-09-20T06:28:14Z

Snehalathak:

'''Title: '''Modeling a Car

'''Author: '''Sejal Dhiman & Arthi Varadarajan

'''Keywords: '''blender 4.1, car modeling, extrude, duplicate objects, combine objects, boolean modifier, video tutorial.

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to this Spoken Tutorial on '''Modeling a Car ''' in '''Blender 4.1'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to model a car using the below options:

* Change the ''' Object ''' name in ''' Outliner'''
* Model using '''Extrude''' option
* Transform objects using '''Object properties'''
* Duplicate objects
* Use '''Boolean modifier'''

|-
|| '''Slide Number 3'''

'''System Requirements'''
|| To record this tutorial, I am using

* '''Mac OS version''' 14.5
* '''Blender version''' 4.1

It is recommended to install '''Blender''' version 4.1 or higher.

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

[https://spoken-tutorial.org/ https://spoken-tutorial.org]
|| To follow this tutorial,

* The learner must be familiar with Blender properties.

|-
||Show Blender
|| I have already opened '''Blender'''.

Let us save our file first.

|-
|| Click on '''File '''and then '''Save'''

Change the folder name to '''Car-animation. '''

Change name as '''Road.blend.'''

Click on '''Save blender file'''
|| Go to '''File '''and select '''Save'''.

Locate and select the '''Car-animation ''' folder which we had saved earlier.

At the bottom change the name '''untitled.blend''' to '''Car.blend'''.

Click on '''Save blender file'''.

|-
||Hover over the cube
|| Let us start making a model of a car.

For that we will use the cube which is selected by default.

|-
||Hover over''' Outliner'''

Change the name to '''Car'''
|| Go to '''Outliner''' on the right side above '''Properties'''.

Objects present in the '''3D viewport''' are listed here.

Double click on the cube and change the name to '''Car'''.

Press''' Enter'''.

|-
|| Hover over the '''Properties '''

Hover over the '''Scale'''

Set the value of '''X '''to''' 2, Y '''to''' 4.5 '''and''' Z '''to''' 0.6. '''

|| First we will scale the cube, by setting the exact dimensions to it.

Go to '''Properties'''.

Observe '''Object Properties''' is selected by default.

In the '''Scale''' option, set the value of '''X ''' to 2, '''Y '''to 4.5 and ''' Z '''to 0.6. Press ''' Enter'''.

|-
|| Hover over the object.

Video editor: '''Tab'''
|| Observe the changes in the object.

Let us start editing the object.

Press '''Tab''' to go to '''Edit mode'''.

|-
|| Video editor: '''Ctrl '''and''' R'''

Hover over the yellow line
|| Now, we will use '''Loop cuts''' to divide the object.

Move the mouse over the object.

Press '''Ctrl ''' and ''' R''' keys together to create the '''Loop Cut'''.

A yellow line appears in the middle of the object.

|-
||Click and move the line
|| Click, and move the line towards the front of the object and click again.

Now the object is divided into two parts.
|-
|| Hover on''' Extrude tool'''
|| We will use the '''Extrude''' option to do the modeling.

'''Extrude''' is a tool that helps to extend or reduce the selected region.

'''E''' is the shortcut key for '''Extrude'''.
|-
|| Go to the '''3D viewport menu >> '''

'''Face selection mode'''
|| Go to the 3D viewport''' menu.'''

Select the '''Face selection mode.'''

|-
|| Video editor: '''E'''

Move the mouse and drag upwards
|| Click on the top right face of the object.

Press '''E '''to extrude.

You will see a blue line and the cursor changes to Move cursor.

Move the mouse and drag the face vertically upwards and click as shown.
|-
|| Click on '''Extrude Region'''

Change '''Z''' value '''to 1.5'''
|| To set the accurate value, go to the bottom left.

Click on '''Extrude Region and Move.'''

Set the '''Z''' value to 1.5 and press '''Enter.'''

|-
||Hold the mouse wheel and move the mouse
|| Hold the mouse wheel and move the mouse to check the object in different views.

|-
|| Video editor:''' E '''

Drag the face outwards

'''Extrude Region >> '''set the '''Z''' value to '''1.6'''
|| There are 2 boxes at the bottom.

Select the backside face of the second box as shown.

Press ''' E'''. Move the mouse, and drag the face outwards as shown and click.

In the '''Extrude Region,''' set the '''Z''' value to 1.6. Press '''Enter'''.

|-
|| Video editor: '''S'''

'''D'''rag the face inwards
|| Next, select the top face of the object. Press '''S'''.

Mouse the mouse, drag the face inwards and click as shown.

|-
|| Go to the '''3D viewport menu >>'''

'''Edge Selection Mode'''

|| Go to the '''3D viewport menu.'''

Select the '''Edge Selection Mode'''.
|-
|| Select the front edge of the top '''face'''

Video editor: '''G '''

Video editor: '''Y'''

Drag the edge backwards
|| Select the front edge of the top '''face''' of the car.

Press '''G '''and '''Y''' keys.

Move the mouse and drag the edge backwards and click as shown.

Now the basic shape of the car is created.

|-
||Only narration
|| Next let us make the doors of the car.

For this, we will use Loop cut again.

|-
|| Press '''numpad 3'''

Video editor: '''Ctrl ''' and '''R'''

|| Press '''numpad 3''' to go to the '''Side view'''.

Keep the mouse in the center of the car and press '''Ctrl '''and '''R''' keys together.

|-
|| Move the line to the front

Zoom in
|| Observe that a '''loop cut''' appears at the center of the car.

Click and move the line towards the front end and click again.

Scroll the mouse wheel outwards to zoom in.

|-
|| Video editor: '''Ctrl '''and '''R'''

Move the line
|| Press '''Ctrl '''and '''R '''again.

Repeat the process and move this line closer to the previous line as shown.

|-
|| Hold '''Shift''' and the mouse wheel together

Move the mouse
|| Hold the '''Shift key''' and the mouse wheel.

Now move the mouse to view the object without changing the angle.

|-
||Create 2 pairs of loop cuts
|| In the similar way, I will create 2 more pairs of lines.

One at the center of the car.

Another pair towards the backside of the car.
|-
|| Go to the '''3D viewport menu'''

'''Face Selection Mode'''

Select the faces

|| Go to the '''3D viewport menu.''' Select the '''Face Selection Mode'''.

Hold the '''Shift key '''and select the '''faces''' of the '''loop cuts'''.

If you select any other face by mistake, press '''Shift''' key and click again to deselect it.

|-
||Select the other side faces
|| Hold the mouse wheel and move the mouse to the other side of the car.

Hold the '''Shift key '''and select the '''loop cut faces''' of this side too.

|-
||Video editor: '''Alt''' and '''E'''
|| Press '''Alt''' and '''E''' keys together.

From the shown menu, select '''Extrude Faces along Normals'''.

Move the mouse and extrude the faces inwards and click.

|-
|| '''Extrude Region and Move'''

Set the '''Z''' value to '''-0.2'''
|| In the '''Extrude Region,''' set the '''Z''' value to -0.2, press '''Enter'''

Observe that the doors are now created.

|-
||Deselect the '''faces'''
|| Next we will design the windows.

Click outside the car to deselect the '''faces'''.

|-
||Select the upper four faces
|| Hold the '''Shift key''' and select all the top four '''faces''' of the doors.

|-
|| Video editor: I

Move the mouse inwards

'''Inset face '''

Set the '''Thickness''' to '''0.03'''
|| Press '''I'''.

'''I''' is the shortcut to inset '''faces''' inside the selection region.

Move the mouse a bit so that the faces turn inwards as shown.

At the bottom, in the '''Inset face''', set the '''Thickness''' to 0.03, press '''Enter.'''

|-
|| Select front and back faces

Video editor: I

Move the '''faces''' inwards

'''Inset faces >> '''

Set the '''Thickness''' to '''0.03'''
|| Select the back '''face''' of the car.

Hold the '''Shift''' key and select the front '''face''' too.

Press '''I'''. Then move the '''faces''' inwards.

In the '''Inset faces''', set the '''Thickness''' to 0.03, press '''Enter '''.

Now we will add some depth to these '''faces'''.

|-
|| Select all 6 upper faces

Video editor: '''Alt '''and '''E'''
|| To do so, hold the '''Shift''' key and select all the 6 top '''faces'''.

Press '''Alt ''' and '''E''' keys together.

|-
|| Select '''Extrude Faces along Normals'''

'''Extrude Region>>'''

Set the '''offset''' to '''-0.02'''

Video editor: '''Tab'''
|| Select '''Extrude Faces along Normals''' from the shown menu.

Now, move the mouse and click to get some depth.

In the '''Extrude Region''', set the '''offset''' to -0.02.

Press '''Enter'''.

Windows of the car are created.

Press '''Tab''' to go to '''Object mode'''.
|-
||Video editor: '''Ctrl''' and '''S'''
|| The car model now resembles a real car.

Press '''Ctrl''' and '''S''' keys together to save our file.

|-
|| Video editor: '''numpad 3'''

Press '''Shift''' and right click
|| Next let’s create spaces in the car to add wheels.

Press '''numpad 3''' to go to '''Side view'''.

Press '''Shift''' and right click to move the '''3D cursor''' in the front region of the car.

|-
|| Video editor: '''Shift''' and '''A'''

'''Mesh >> Cylinder'''
|| Press '''Shift''' and '''A''' keys together to open the '''Add''' menu.

Select '''Mesh'''.

Then click on '''Cylinder'''.

|-
|| Click on '''Add cylinder'''

Set the '''Vertices''' to '''24'''
|| Go to the bottom left.

Click on '''Add cylinder''' option.

Set the '''Vertices''' to 24.

In''' Rotation '''set the ''' Y '''value to 90.

Press''' Enter'''.

|-
|| Video editor: '''Z'''

Select '''Wireframe'''
|| Press '''Z''' to open '''Viewport shading modes'''.

Select '''Wireframe'''.

This helps to place the '''cylinder''' accurately since only the edges are visible.

|-
|| '''Object Properties >> '''set '''X, Y & Z''' values to '''0.6'''

Video editor: '''G'''
|| Let us resize the '''Cylinder.'''

Go to '''Object Properties'''.

In the '''Scale''' option, change the X, Y and Z values to 0.6. Press '''Enter'''.

Press '''G ''' and move the '''cylinder''' as shown.

Three fourths of the cylinder should be inside the car.

|-
||Video editor: '''numpad 7'''
|| Press '''numpad 7''' to go '''Top view '''.

Make sure that half of the cylinder should be inside the car.
|-
|| Video editor: '''Shift''' and '''D'''

Video editor: '''G'''

Video editor: '''Y'''
|| Next we will duplicate this cylinder and add it to the back side of the car.

Press '''Shift''' and '''D ''' keys together.

Press '''G''' and '''Y''' keys and move the duplicated cylinder to the back side.

|-
|| Video editor: '''Shift''' and '''D'''

Video editor: '''G'''

Video editor: '''X'''
|| Hold the '''Shift''' key and select both the cylinders.

Press '''Shift''' and '''D '''keys together.

Press '''G''' and '''X keys''' and move them to the other side of the car as shown.
|-
|| Video editor: '''Z'''

Select '''Solid mode'''
|| Now we will create space for the wheels.

Press '''Z ''' to open the '''Viewport Shading modes'''.

Select '''Solid'''.

Hold the '''Shift''' key and select all the four cylinders.

|-
||Video editor: '''Ctrl''' and '''J'''
|| Press '''Ctrl''' and '''J''' keys together to group them together.

Again hold the '''Shift '''key and select the car too.

|-
|| '''Properties >> Modifiers (spanner icon)'''

Click on '''Add modifier'''

'''Generate >> Boolean'''
|| Go to '''Properties'''.

Select ''' Modifiers'''.

Click on '''Add modifier'''.

From the dropdown, select '''Generate''' and click on '''Boolean'''.

|-
|| Click on the '''Object field '''

Select '''Cylinder.001'''

Click on the dropdown arrow next to the

'''Boolean field >> Apply'''

Video editor: '''X'''

|| Make sure that the '''Difference ''' option is selected.

Click on the '''Object field'''.

Select '''Cylinder'''

Click on the dropdown arrow next to the '''Boolean field.'''

Select '''Apply'''.

Now click on the cylinders.

Press '''X''' and '''Delete ''' from the shown menu.

|-
|| Hold the mouse wheel and move the mouse
|| Hold the mouse wheel and move the mouse to change the view.

Observe that the cylinders are gone creating a difference in the car.

We will add wheels in these spaces in the upcoming tutorials.

|-
||Video editor: '''Ctrl''' and '''S'''
|| Press '''Ctrl''' and '''S ''' keys together to save the file.

With this we have come to the end of this tutorial.

Let us summarize.

|-
||'''Slide Number 5'''

'''Summary'''

|| In this tutorial, we have learnt to model a car using the below options:

* Change the ''' object ''' name in ''' Outliner'''
* Model using '''Extrude''' option
* Transform objects using '''Object properties'''
* Duplicate objects
* Use '''Boolean modifier'''

|-
||'''Slide number 6'''

'''Assignment'''
|| As an assignment, please do the following:

Create a Jeep Model in '''Blender'''.

The Jeep model should look like this.

|-
|| '''Slide Number 7'''

'''About the Spoken Tutorial Project'''
|| The video at the following link summarizes the '''Spoken Tutorial project'''.

Please download and watch it.
|-
|| '''Slide Number 8'''

'''Spoken Tutorial workshops'''

|| The '''Spoken Tutorial Project''' team conducts workshops and gives certificates.

For more details, please write to us.
|-
|| '''Slide Number 9'''

'''Answers for THIS Spoken Tutorial'''
|| Please post your timed queries in this '''forum'''.
|-
|| '''Slide Number 10'''

'''FOSSEE Forum'''
|| For any general or technical questions on '''Blender''', visit the '''FOSSEE forum''' and post your question.
|-
|| '''Slide Number 11'''

'''Acknowledgement'''
|| '''The Spoken Tutorial''' project was established by the '''Ministry of Education''', '''Government of India'''.
|-
||
|| This is Arthi along with Sejal from '''IIT Bombay''' signing off.

Thanks for joining.
|-
|}

AutoDock4/C2/Running-AutoGrid/English

2024-09-05T12:09:57Z

Snehalathak:

'''Title of script''': Running AutoGrid

'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''

{| border =1
|| Visual Cue
||Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Running AutoGrid'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to,

* Set the grid box parameters
* Create a grid for the receptor molecule
* Save the grid box properties as .gpf file.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
||
* Run the AutoGrid program
* Check the output '''.glg''' file for the successful running of the ''' AutoGrid''' program.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using,

* '''Ubuntu Linux '''OS version 20.04

* '''AutoDockTools''' version 1.5.7

* Gedit version 3.36.2

Windows users may use notepad or any other text editor.

|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on AutoDock Tools interface

|-
|| '''Slide number 6'''

'''Code Files'''

||
* The input files required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 7'''

'''Code Files'''
||
* Save the input file in your home directory or working directory.
* Make a copy of all the files and then use them for practising

|-
|| Open the terminal using “Show Applications” button.

Type '''adt''' at the prompt.

Cursor on ADT interface.
|| Here, I have opened the AutoDock Tools interface.

|-
|| Cursor on the ADT interface.
|| I will open the session saved previously while preparing the receptor for docking.

Please watch the pre-requisite tutorial on preparing the receptor for docking.
|-
|| Click on '''File''' then '''Read Session''',

from the '''Read Pmv Session''' pop-up box, select,

'''2vta-receptor-prep.psf''' file.

Click on '''Open''' button.
|| Click on '''File''' then choose '''Read Session.'''

'''Read Pmv Session''' dialog-box opens.

I will select '''2vta-receptor-prep.psf''' file which I had saved in my home directory.

Click on the '''Open''' button.
|-
|| Click on '''Grid '''tab on the menu bar.

Click on '''Macromolecule''' and '''Choose''' option.

|| The model of the receptor molecule appears on the panel.

To create the grid, click on ''' Grid tab '''on the''' '''menu bar.

Select '''Macromolecule''' and click on '''Choose''' option.

|-
|| In the '''Choose Macromolecule''' pop-up box, click on '''2vta.'''

Click on '''Select Molecule '''button at the bottom of the pop-up box.

|| In the '''Choose Macromolecule''' dialog-box click on '''2vta'''.

Click on the '''Select Molecule '''button at the bottom of the dialog-box.
|-
|| Cursor on the pop-up window.
|| A '''WARNING''' pop-up window appears describing the following;

<nowiki>* the number of non-bonded atoms, which ideally should be zero.</nowiki>

<nowiki>* the number of non-polar hydrogen atoms found, </nowiki>

* Note that the non-polar hydrogens, nphs have been merged.

|-
|| Click '''OK'''

Cursor on pop-up window '''Modified AutoDock4 Macromolecule File.'''

Click on '''Save''' button.

|| Click '''OK''' to close the pop-up.

Another pop-up window '''Modified AutoDock4 Macromolecule File''' opens.

Save the receptor as a .pdbqt file.

We need to use only the '''PDBQT '''file format for creating the grid.

Click on '''Save''' button.

|-
|| Cursor on the '''ADT''' panel.
|| Notice the change in the appearance of the receptor.

The '''gasteiger''' charges are also calculated for each atom.

|-
|| Click '''Grid''' then on '''Set Map Types''',

'''Open Ligand''' option.

In the Ligand File window, select '''ligand.pdbqt''' file.

Click on the Open button.

|| Now let us add the ligand to the receptor.

Next click '''Grid''' then on '''Set Map Types''' and '''Open Ligand''' option.

A '''Ligand File''' window opens, select '''ligand.pdbqt''' file and click on '''Open''' button.

|-
|| Cursor on the ADT panel.
|| You can now see that ligand is added to the receptor.

On the panel you can see receptor and ligand complex.

|-
|| Cursor on the ADT interface.
|| Next we must prepare the '''grid box ''' for this '''receptor-ligand''' complex.

For this we must set the '''grid box''' parameters.

|-
|| '''Slide Number 8 '''

'''About Grid Box '''

The grid box set the boundary of the docking.
|| About the Grid Box.

The grid box position defines the region of the receptor where the docking will be performed.

Any region outside the box won't be explored during docking.

|-
|| '''Slide Number 9'''

'''About Grid Box '''

|| However, we must first know the region of the receptor containing the ligand binding site.

Learners must go through the literature for the information on the ligand binding site.

|-
|| '''Slide Number 10'''

'''About Grid Box'''

'''Learners please note:'''

In case we do not know the exact coordinates for grid box, visualize the active site residues
and set the grid boxes centering these residues.

A blind docking covering the entire receptor can also be performed.

|| If the active site information is unknown, it is recommended to search all available surfaces.

In such a case the grid box should cover the whole receptor-ligand complex.

|-
|| Click '''Grid >> Grid Box'''.

'''Grid Options''' window opens.
|| Back to the '''ADT''' interface.

To set the grid box, click on '''Grid '''and then select '''Grid Box'''.

'''Grid Options''' window opens.

This will open up a menu-interface with some default options.

|-
|| Cursor on the ADT interface.
|| On the panel you can now see the grid box covering a certain portion of the receptor.

We need to set the center of the grid as well as the x,y,z dimensions of the grid.

|-
|| Cursor on the ADT interface.
|| Sometimes we may not know the active site information.

In such a case a blind docking covering the entire receptor can be performed.
|-
|| Rotate the slider towards the right in x, y and z directions to reach 126 points.

Cursor on the receptor-ligand complex.
|| In the Grid Options window, you can rotate the slider in x,y and z directions to cover the entire receptor-ligand complex.

Click and drag the slider towards the right in x, y and z directions.

Drag until you reach maximum capacity 126 points.

As shown here we have the grid box covering the entire protein.

|-
|| Cursor on the ADT interface.
|| In the present example, we already know the coordinates corresponding to the ligand binding site.

|-
|| Rotate the slider towards the right on x, y and z direction to reach 50,

(from 126 points to 50 points)
|| Rotate the slider to change the number of points on x, y and z directions to 50.

Click the slider and drag the mouse from right to left to decrease the number.
|-
|| Cursor on the ADT interface.
|| Observe the grid box, it is now smaller in size.

Also observe that the grid box is not centered on the active site.
|-
|| Change the numbers in the '''Center Grid Box.'''

Change the Coordinates of the center of the binding site in the x, y and z direction to 27.86 , 0.69, 66.23.

'''site-specific docking, '''
|| To center the grid box over the active site, change the numbers in the '''Center Grid Box'''.

Change the coordinates of the center of the binding site in the x, y and z directions.

I will type the numbers in the fields given.

Type 27.86, 0.69, 66.23 in the x, y and z directions.

Here too we can use the slider to change the numbers.

|-
|| Cursor on the ADT interface.
|| Observe the panel, now the grid box is centered on the active site.
|-
|| Click File in the top-left of the '''Grid Options''' window,

choose '''Close saving current.'''
|| To save the grid box properties, click on '''File''' in the top-left of the '''Grid Options''' window.

From the options choose '''Close saving current.'''

The''' Grid Options''' window closes.
|-
|| Cursor on the '''ADT''' panel.
|| '''AutoGrid''' requires an input grid parameter file, which usually has the extension ''' .gpf.'''

The grid parameters you just set need to be saved as a .gpf file.
|-
|| Click '''Grid '''on the main on the ADT interface.

From the options choose '''Output'''. Select '''Save GPF.'''

'''Grid Parameter Output File''' window opens.
|| Click '''Grid '''on the menu bar on the ADT interface.

From the options choose '''Output'''.

Select '''Save GPF'''.

'''Grid Parameter Output File''' window opens.
|-
|| Type the file name as '''2vta.gpf.'''

Click on '''Save '''button at the bottom-right in the '''Grid Parameter Output File''' window.

Save the file as '''2vta.gpf.'''
|| Type the file name as '''2vta.gpf'''.

'''Files of type '''field is already autofilled as gpf file.

Click on '''Save ''' button at the bottom-right in the '''Grid Parameter Output File''' window.

The file will be saved in your home directory as '''2vta.gpf'''.

|-
|| click on '''Run''' on the menu bar.

Choose '''Run AutoGrid''' from the drop down.

Cursor on '''Run AutoGrid''' window.

|| To run AutoGrid, click on '''Run''' on the menu bar.

Then choose '''Run AutoGrid''' from the drop down.

'''Run AutoGrid''' window appears.

Here you will notice that various fields are auto populated.

|-
|| Cursor on '''Run AutoGrid''' window.
|| '''Windows''' users may click on the '''Browse''' button next to '''Program Pathname'''.

They can then choose the location of '''autogrid4.exe.'''

|-
|| Cursor on '''Run AutoGrid''' window.
|| Alternatively, you can copy and paste the '''autogrid4.exe '''file to your working directory.

I am using '''Linux '''.

Hence I will leave it as such as my '''Program Pathname '''is already auto-populated.

|-
|| In the''' Run AutoGrid''' window, Click on the '''Browse '''button next to the '''Parameter Filename''' field.

Select '''2vta.gpf '''from the home folder.

click on the '''Open''' button.
|| Next is '''Parameter Filename'''.

I will click on the '''Browse ''' button next to the '''Parameter Filename''' field.

'''autogrid4 Parameter File''' dialog box opens.

I will select '''2vta.gpf '''from my home folder and

click on the '''Open''' button.
|-
|| Cursor on the '''Log Filename''' field.
|| '''Log Filename''' field will be automatically populated as '''2vta.glg'''.

Leave the rest of the parameters at the default setting.
|-
|| Click on the '''Launch''' button.

Cursor on the “'''Autodock Process Manager” '''window.
|| Click on the '''Launch''' button.

A popup entitled “'''Autodock Process Manager'''” will appear.

This popup will automatically close when the process ends.
|-
||Open home folder. Cursor on home folder.

Cursor on''' .map''' files.

|| When the popup closes, '''AutoGrid''' has completed the generation of receptor maps.

I will open my home folder and check for a number of files with the extension '''.map'''.

Notice the number of files with '''.map''' extension.

We also must locate the '''2vta.glg''' file.

Learners please note:

Do not delete any of the output files generated during the running of the autogrid program.

These files will be required for the next step, which is running of the autodock program.

|-
|| Cursor on .map files.

Right click on 2vta.glg file, choose, Open with Text Editor option.

Scroll down the pages.

Cursor on the line '''autogrid4: Successful Completion.'''

Cursor on the '''.glg file'''.

|| To make sure autogrid is successfully completed, open the '''.glg''' file using a text editor.

Right click on the '''2vta.glg''' file and choose, '''Open with Text Editor''' option.

Scroll down the pages to the last line in the document.

Here you can see the message, '''autogrid4: Successful Completion'''.

Close the '''glg''' file.

|-
|| Only Narration
|| This brings us to the end of this tutorial.

|-
|| '''Slide Number 11'''

'''Summary Slide'''

|| Let's summarize,

In this tutorial, we have,

* Set the grid box parameters
* Created the grid for the receptor molecule
* Saved the grid box properties as .gpf file

|-
|| '''Slide Number 12'''

'''Summary Slide'''

||
* Ran the AutoGrid program
* Checked the output .glg file for the successful running of the AutoGrid program

|-
|| '''Slide Number 13'''

'''Assignment'''

|| As an assignment

Run the autogrid for the example, '''1DWD''' given in the Examples folder in the Downloads page.

https://autodock.scripps.edu/download-autodock4/

|-
|| '''Slide''' '''Number 14'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide''' '''Number 15 '''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.
|-
|| '''Slide''' '''Number 16'''

'''Forum'''
||
* Please post your timed queries in this forum.

|-
|| '''Slide''' '''Number 17'''

'''Acknowledgement '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
||'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Getting-Started-with-Docking/English

2024-09-04T12:20:24Z

Snehalathak:

'''Title of script''': '''Getting Started with Docking'''

'''Author''': Dr.Snehalatha Kaliappan and Sruthi Sudhakar.

'''Keywords''': autodock4, adt, mgl tools, ligand, receptor, rcsb protein data bank, ligand refinement, add hydrogens, detect root, rotatable bonds, pdb file, pdbqt file, video tutorial.

{| border =1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
||'''Slide Number 1'''

'''Title Slide'''
||Welcome to this tutorial on '''Getting Started with Docking'''.
|-
||'''Slide Number 2'''

'''Learning Objectives'''
||In this tutorial, we will learn to

* Download ligand and receptor files from the database
* Perform ligand refinement using '''AutoDockTools'''
* Prepare ligand for docking
* Save the refined ligand as a pdbqt file

|-
||'''Slide Number 3'''

'''System Requirement'''
||Here I am using,

'''Ubuntu Linux '''OS version 20.04

'''AutoDockTools''' version 1.5.7

'''Google Chrome browser''' version 96.0.4

And a working internet connection

|-
||'''Slide Number 4'''

'''Pre-requisites'''
||To follow this tutorial learner should be familiar with,

basic computer operations, and

basic bioinformatics

|-
||Open web browser, in the address bar type, '''rcsb.org''

Press Enter.

[https://www.rcsb.org/ https://www.rcsb.org/]
||Open any web browser.

We will now download the '''ligand''' and '''receptor''' files from '''Protein Data Bank'''.

In the address bar type, '''rcsb.org'''

and Press Enter

'''Protein Data Bank ''' website opens.

|-
||https://www.rcsb.org/structure/2VTA

Type '''2VTA''' in the search field.

Click on the search button.

Cursor on the page.
||In the search field at the top, type the 4 letter '''PDB code 2VTA'''.

Click on the search button on the right.

The page refreshes with the 3D model and information about the protein.

'''2VTA''' codes for a '''Cyclin Dependent Kinase'''.

|-
||Cursor on the blue Download Files button.

Click the Download Files button and select '''PDB format.'''

||On the right-side of the page, you will see a '''Download Files''' button.

Click on the white triangle next to the button.

From the drop down options select '''PDB format'''.

|-
||Show the pdb file, '''2vta.pdb''' in the '''Downloads''' folder.
||The PDB file '''2vta.pdb ''' for the protein '''2VTA ''' downloads to your '''Downloads''' folder.

|-
||Scroll down the page,

Cursor on '''Small Molecules ''' section.

Under '''Ligands ID''', '''LZ1 ''' click on '''Download Instance Coordinates''', from the options in the drop down.

Choose '''MOL2 format, Chain D.'''

||Scroll down the page, in the '''Small Molecules ''' section under '''Ligands ID''' you will see '''LZ1'''.

Click on the '''Download Instance Coordinates ''' drop down.

From the options in the drop down, choose '''MOL2 format''', '''Chain D'''.

|-
||Show the mol file '''2vta_D_LZ1.mol2'''
||The mol file for the ligand downloads to the '''Downloads ''' directory in my system.

Here is my '''Downloads''' directory.

Here are the two downloaded files from the '''PDB website''', the mol file and the pdb file.

|-
||Click on the files '''2vta.pdb''' and '''2vta_D_LZ1.mol2'''.

Use '''Ctrl + X'' key to cut and '''Ctrl + V''' keys to paste the files.

||I will move both the downloaded files to my '''home directory'''.

I will select both the files and right-click.

From the options choose ''' Move to''' option.

'''Select Move Destination''' window opens.

I will select my '''home folder''' and click on the '''Select''' button at the top-right corner.

We can alternatively use '''Ctrl''' and '''X''' keys to cut and '''Ctrl''' and '''V''' keys to paste the files.

|-
||Open the terminal using the show applications icon.
||The next step is ligand refinement.

Open '''AutoDockTools''' also called '''ADT''' .

I will open '''ADT''' using the terminal.
|-
||At the terminal prompt type '''adt '''and press Enter.

Type the system password.
||I am using the Ubuntu 20.04 system.

Hence I will click on the '''Show Applications''' button at the bottom-left.

On the search bar that appears I will type '''Terminal'''.

Then click on the '''terminal''' option on the screen.

The terminal opens.

At the prompt I will type ''' adt ''' and press Enter.

Type the system password when prompted.

|-
||Cursor on ADT interface.

Click on '''File''' >> '''Preferences'''

>> '''Set'''.

In the '''Set User Preferences''' window, go to '''Startup Directory'''.

For me path is,

'''/home/snehalatha'''

|| Click on “'''Remind me later'''”.

'''ADT''' interface opens.

Set up your startup or working directory by going to '''File''' >> '''Preferences ''' and then ''' Set'''.

In the '''Set User Preferences window''' look for the '''Startup Directory ''' field.

Here we need to set the path to the folder where we need to save the output files.

I am setting the path to my home directory.

Click on '''Make Default''', and then click on '''Dismiss'''.

|-
||Click on the Ligand tab on the menu bar (last row in the menu bar)

Choose '''Input''' and then click on the Open option.

||To refine the '''ligand,''' click on '''Ligand ''' tab on the menu bar.

Choose '''Input''' and then click on the '''Open''' option.
|-
|| In the '''Ligand file for AutoDock4''' , open '''2vta_D_LZ1.mol2 file'''.

Click on the Open button at the bottom-right.

||The '''Ligand file for AutoDock4''' dialog box opens.

Since I have set the path for the home directory, the folder opens by default.

We need to open '''mol2''' file.

So select '''Files of Type''' as '''Mol2''' files from the drop-down.

Select the '''mol2''' file of the ligand, '''2vta_D_LZ1.mol2'''

Click the '''Open''' button at the bottom-right.
|-
||Cursor on the display panel.

Cursor on the pop-up window.

Click on '''OK'''.
||The structure will appear in the display panel on the ADT interface.

A popup window titled '''Summary for 2vta_D_LZ1''' will appear.

The message with information about the structures will be displayed.

Read the message and note the information.

Click on OK button.
|-
|| Click on '''Edit''' menu, select '''Hydrogens''', then select '''Add''' option.

In the''' Add Hydrogens''' dialog box select radio button '''All Hydrogens.'''

Click on '''OK'''.

Cursor on the structure.
||Since this structure was derived from the '''protein data bank''', it does not contain hydrogens.

Click on the Edit menu, and select '''Hydrogens''', then select '''Add''' option.

'''Add Hydrogens''' dialog box opens, select '''All Hydrogens '''radio button'''.

Leave all other settings as such and click on the '''OK'''.

You will now notice that hydrogens are added to the structure on the panel.

|-
||'''Slide Number 5 '''

'''Adding Hydrogens'''
||This step can be ignored in cases where the ligand structure is generated by other means such as:

'''quantum mechanical optimization''' or

draw the 2D structure and convert to 3D in '''Open Babel'''.

In the above cases the hydrogens are automatically added.

|-
||Go to '''File''' menu, >> '''Save''' >> '''Write PDB'''.

Cursor on''' Write options''' dialog box.

Type the file name as '''Ligand.pdb'''

Cursor on '''Browse''' button.

Click '''OK''' to close the dialog box.
||Now we have to save this structure in pdb format.

Go to '''File''' menu select '''Save''' option.

From the sub-menu select '''Write PDB'''.

'''Write options''' dialog box opens.

File name with .pdb extension and path to my working directory will be automatically populated.

Change the file name as '''Ligand.pdb'''

You can use the '''BROWSE''' button If you want to save in any other location.

Click '''OK''' to close the dialog box.
|-
||Cursor on''' ADT''' interface.
|| Now we need to prepare the ligand for docking.

|-
||Close the window by File >> Exit

In the '''Quit '''dialog box, Do you wish to Quit?

click on '''OK'''.

||Let us close the existing ADT window.

Go to '''File''' menu and click on '''Exit''' option.

In the '''Quit ''' dialog box, Do you wish to Quit?

click on '''OK''' button.
|-
||At the terminal prompt type '''adt''' and press Enter.
||To open a new ''' ADT''' interface use the terminal as we did before.

At the terminal prompt type '''adt''' and press Enter.

Click on “'''Remind me later'''” .

'''ADT''' window opens.

|-
||Go to '''Ligands''' menu >> '''Input''' >> '''Open'''.
||Go to '''Ligands''' menu.

Click on '''Input''' then click on '''Open'''.

Since we have already saved the working directory, it is the default directory now.

|-
||Select '''Files of Type''' as '''PDB''' files from the drop-down.

Select '''Ligand.pdb''', and click '''open'''.
||Select '''Files of Type''' as '''PDB''' files from the drop-down.

Select '''Ligand.pdb,''' and click '''open ''' button.
|-
||Cursor on the adt display panel.
||The structure will appear in the display panel of '''ADT'''.

A pop-up window titled''' summary for Ligand''' will appear.

Read the message and click '''Ok''' to continue.
|-
||Click '''Ligand''' >> '''Torsion Tree ''' >> '''Detect Root'''.

Cursor on the green sphere on nitrogen atom.

||Click '''Ligand and '''select '''Torsion Tree '''then choose '''Detect Root.'''

A green sphere will appear over the '''indazole''' Nitrogen atom.

This is the '''torsion root''', or the '''center of rotation ''' within the molecule.

This is a step to define the allowed '''torsions'''.

|-
||Click '''Ligand '''>> '''Torsion Tree''' >> '''Choose Torsions'''.

Cursor on '''Torsion Count''' dialog box.

All the bonds are red, cursor on bonds.

Click '''Done '''to close the window.
||To visualize which bonds are allowed to be rotatable,

Click on '''Ligand''', and select '''Torsion Tree''' then '''Choose Torsions'''.

'''Torsion Count''' dialog box opens.

This will change the color of all the bonds to demonstrate which are rotatable.

Here we see the number of rotatable bonds as Zero.

The parameters can be changed to fix the specific bonds.

Also allow additional degrees of freedom in ligand molecules.

Click '''Done ''' to close the window.
|-
||Click '''Ligand''' >>''' Output''' >> ''' Save as PDBQT'''.

A dialog box opens, file name is auto populated as ligand.pdbqt.

Click on '''Save''' button.

||'''Save''' the file as a '''.pdbqt''' file.

Click on '''Ligand''', and select '''Output'''.

Then select '''Save as PDBQT'''.

A dialog box opens, file name is auto populated as '''ligand.pdbqt'''.

Click on '''Save''' button.

This completes the step of ligand refinement using '''AutoDock Tools'''.
|-
||'''Slide Number 6'''

'''Summary slide'''
||Let us summarize,

In this tutorial we have,

Downloaded ligand and receptor files from the database.

Performed the ligand refinement using '''AutoDockTools'''.

Prepared the ligand for docking.

Saved the refined ligand structure as '''pdbqt''' file format using '''ADT'''.
|-
||'''Slide Number 7'''

'''Assignment-1'''
||As an assignment

Read about the docking process.

Use the link given here for more information.

https://ccsb.scripps.edu/projects/docking/

|-
||'''Slide Number 8'''

'''Assignment-2'''
||

Download the ligand and receptor files from the PDB database for 1DWD

Do the ligand refinement and create the pdbqt file for 1DWD

|-
||'''Slide Number 9'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
||'''Slide Number 10'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please contact us.

|-
||'''Slide Number 11'''

'''Answers for THIS Spoken Tutorial '''
||
* Do you have questions in THIS Spoken Tutorial?
* Please visit this site
* Choose the minute and second where you have the question.
* Explain your question briefly
* The spoken tutorial project will ensure an answer.
* You will have to register on this website to ask questions.

|-
||'''Slide 12'''

'''Acknowledgement '''
||Spoken Tutorial project was established by Ministry of Education (MoE), Govt. of India
|-
||
||This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

Blender-4.1/C3/Creating-a-Road/English

2024-09-03T06:45:44Z

Snehalathak:

'''Title: '''Creating a Road

'''Author:''' Sejal Dhiman & Arthi Varadarajan

'''Keywords: '''blender 4.1, object mode, edit mode, loop cut, material, bezier curve, array modifier, curve modifier, solidify, video tutorial.

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide '''
|| Welcome to the '''Spoken tutorial''' on '''Creating a Road '''in''' Blender 4.1'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
||In this tutorial, we will learn to create a road using the options given here:

* Add and edit a''' plane'''
* Use '''Loop cut'''
* Use '''Viewport Shading modes'''
* Add '''Material''' to an object
* Use '''Array''', '''Curve''' and '''Solidify''' '''modifiers'''

|-
|| '''Slide Number 3'''

'''Software and System Requirement'''
||To record this tutorial, I am using

* '''Mac OS version 14.5 '''
* '''Blender version''' '''4.1'''

It is recommended to install '''Blender version 4.1''' or higher.

|-
|| Slide Number 4

'''Pre-requisites'''
||To follow this tutorial
* The learner must know to add objects in Blender.

|-
|| Blender interface
||I have already opened Blender.

|-
|| Video editor: '''X'''

Click on '''Delete.'''

The cube has to be selected.
||Let us start creating the road.

First we will delete the '''cube'''.

Press''' X '''and select '''Delete''' from the shown menu.
|-
|| Cursor on the 3D view port.
|| Next, let us add a plane for creating the road.
|-
|| Video editor: '''Shift''' and '''A'''

'''Mesh >> Plane'''

||Press '''Shift '''and''' A '''keys together to open the ''' Add '''menu.

Select '''Mesh''' and then click on '''Plane '''.

|-
|| Video editor: '''numpad 7'''
||Let us go to the '''Top view''' to work further.

For this, press '''numpad 7''' to show the top view.
|-
|| Go to the '''Toolbox. '''Click on '''Scale'''

Drag the green handle upward
||Next, let us resize the plane.

Go to the '''Toolbox''' and click on '''Scale '''.

Click on the green handle of the gizmo and drag it upwards.

|-
|| Hover over '''Resize''' option
||To set the exact dimension, go to the bottom left.

Observe that, '''Resize''' option is available as the '''Scale tool''' is used.

This option may vary as per the action performed on the '''3D viewport'''.

|-
|| Click on the '''Resize. '''

Change the value of '''Y''' to '''3.5'''
||Click on the '''Resize''' option.

Change the value of '''Y''' to '''3.5. '''Press '''Enter.'''

Observe the change in the '''plane.'''

|-
|| point to the plane.
||Note that we are currently working in the '''Object Mode'''.

To edit the object, we need to go to '''Edit mode. '''
|-
|| Hover over the top left slide corner

Click on '''Object mode drop down.'''

Click on '''Edit mode'''

Press '''Tab''' key twice
||Go to the top left corner.

Below the '''Menu, '''locate the dropdown named '''Object Mode'''.

Click on it and select '''Edit mode'''.

'''Tab''' key also helps to switch between '''Object mode''' and '''Edit mode.'''
|-
|| Point to the 3 icons.
||Next to the '''Edit mode''' option, observe the three icons.

|-
|| Click on '''Vertex selection mode'''
|| In '''Vertex selection mode,''' we can edit the vertices of the object.
|-
|| Click on '''Edge selection mode'''
|| In '''Edge selection mode,''' we can edit the edges.
|-
|| Click on '''Face selection mode'''

Click on''' Edge selection mode'''
||'''Face selection mode '''allows to work and edit the faces of the object.

For now, I will select '''Edge selection mode.'''

|-
|| Hover over the plane
||Now let us add '''loop cuts''' to the plane.

|-
|| Go to '''Tool box.''' Click on '''Loop Cut '''
||For that, go to the '''Toolbox''' and click the '''Loop Cut'''.

Move the mouse onto the plane.

|-
|| Click when yellow line appears vertically on the '''plane'''
||You can see a yellow line appearing over the plane.

When it appears vertically, click on it.

Observe that an edge is created in the middle of the plane.

|-
|| Hover over the plane
||Now, we will add another vertical edge.

|-
|| Hover over the bottom left corner

Click on '''Loop Cut and Slide'''

Set the '''Number of Cuts '''to '''2'''

||To do so, go to the bottom left.

On the''' Loop Cut and Slide '''option, set the '''Number of Cuts''' to '''2'''. Press''' Enter.'''

I will minimize this option.

Now you can see two vertical edges on the '''plane.'''
|-
|| Go to '''Tool box.''' Click on '''Scale.'''

Drag the red handle towards the right side.

||Let us move these edges towards the corner of the plane.

Go to the '''Toolbox''' and click on '''Scale'''.

Click and drag the red handle towards the right side.

|-
|| Release the mouse button
||Once the lines move to the corner of the plane, release the mouse button.

|-
|| Hover over the plane

Click on '''Loop Cut'''
||Next, let’s add horizontal edges to the plane.

Go to '''Toolbox.''' Click on '''Loop cut.'''

|-
|| Click to create horizontal loop cut
||Move the mouse on the plane.

When the yellow line comes horizontally, click on it.

Let us add 3 more edges to the plane.

|-
|| Go to the bottom left corner

Click on '''Loop Cut and Slide'''

Set '''Number of Cuts''' to '''4 '''
||Go to''' Loop Cut and Slide '''option.

Change the '''Number of Cuts''' to 4 and press''' Enter.'''

We see four horizontal edges created to the plane.

|-
|| Go to '''Toolbox.'''

Click on the '''Select Box'''.

||Let us align these edges now.

Go to '''Toolbox''', Click on the '''Select Box'''.

|-
|| Click and drag on the first edge
||Click and drag the mouse on the first horizontal edge and select it.

|-
|| Hold '''Shift '''key. Click and drag on the last edge
||Hold the '''Shift''' key and drag the mouse over the last horizontal edge as shown.

|-
|| Hover over the selected edges
||Let us now move these edges towards the corner of the plane.

|-
|| Go to '''Tool box.''' Click on '''Scale.'''

Select and drag it vertically upward
||Go to '''Toolbox''', Click on '''Scale. '''

Click on the green handle of the gizmo and drag it vertically upwards as shown.

|-
|| Click on '''Select box tool.'''

Select the second and third created edges of the plane
||Let us align the other 2 edges. Click on the '''Select box tool.'''

Click and drag to select the second edge of the plane.

Hold the '''Shift''' key and select the third edge.

|-
|| Click on '''Scale tool.'''

Move the edges closer
||Click on the '''Scale tool.'''

Move them close to each other using the green handle as shown.

|-
|| Only narration
||Next, let’s add some colors to the plane to make it look like a road.

|-
|| Video editor: '''Z'''
||To preview the changes, we will make use of the '''Viewport Shading Modes'''.

Press '''Z''' key to open the '''Viewport Shading Modes.'''

|-
|| Hover over '''Solid mode'''

Click on''' Material preview'''
||Currently, '''Solid mode '''is active.

We will change it to '''Material Preview mode'''.

Let us add '''materials''' to the plane now.
|-
|| Go to '''Properties'''
||Go to the '''Properties '''panel''' on the right.

Keep the cursor near the left corner of the '''Properties '''panel.

A double headed arrow appears
|-
|| Click and drag on the double headed arrow.

Click on '''Materials. '''

|| Click and drag the double headed arrow towards the left.

Like this we can resize the panels in '''Blender.'''

Click on the last circular icon called '''Material.'''

|-
|| Click on''' New'''
||The '''Material properties '''open on the right side.

Click on '''New.'''

|-
|| Replace '''Material001 '''with '''Road'''

Click on the '''Base Color'''
||Change the '''Material001 '''name to''' Road. '''Press '''Enter.'''

Click on the '''Base Color '''field.
|-
|| Hover over the color wheel

Select black color

Move the mouse
||A color wheel appears.

Drag the mouse and select black color as shown.

Move the mouse outside the color wheel.
|-
|| Hover over the road
||You can see that the color of the road changes to black.

|-
|| Only narration
||Let’s now make it realistic by adding more details to it.

|-
|| Click on '''Select box tool'''

Select the middle box
||Click on the '''Select box tool.'''

Then drag and select the middle face of the '''plane.'''
|-
|| Go to '''Properties. '''

Click on “+”.

Select '''New'''

Change the '''Material001''' to '''Yellow stripe'''

||Go to the '''Properties. '''

Click on the “+” option. Click on '''New'''.

In the name field, change '''Material001''' to '''Yellow stripe'''.

Press '''Enter.'''
|-
|| Click on the '''Base Color '''field

Select yellow color

Click on '''Assign'''
||Click on the '''Base Color '''field. Color wheel opens.

Choose the shade of yellow that resembles the yellow lines on a real road.

Click on '''Assign. '''

Observe the color changes to yellow of the selected face of the plane.

|-
|| Drag and select the horizontal top 3 boxes.

Hold the '''Shift '''key and select the horizontal bottom 3 boxes too.

||Let us now add white lines on the sides of the road.

Drag and select the horizontal top faces.

Hold the '''Shift '''key and select the horizontal bottom faces too.
|-
|| Go to '''Properties.'''

Click on “+”.

Select '''New'''

Change the '''Material001''' to '''White stripe'''

||Go to '''Properties. '''

Click on the “+” option. Click on '''New'''.

In the name field, change the '''Material001''' to '''White stripe'''.

Press '''Enter. '''We can keep the default white color here.

|-
|| Click on '''Assign'''
||Click on '''Assign'''.

Now the color changes to white on the selected area of the plane.

|-
|| Hover over the road
||Let us now convert this straight road to a curved road.

|-
|| Press '''Tab''' key
||Press '''Tab''' key to change the '''Edit mode''' to '''Object mode.'''

Next, let us add a curve to the '''3D viewport'''.

|-
|| Video editor: '''Shift '''and''' A'''

Select '''Curve. '''Click on '''Bezier'''
||Press '''Shift '''and''' A''' keys together.

Select '''Curve''' and then on''' Bezier'''.

Scroll the mouse wheel inwards to zoom in and view the curve properly.
|-
|| Click on '''minus''' key
||Let’s increase the size of the curve.

Scroll the mouse wheel outwards to zoom out the view as shown.

|-
|| Video editor: '''S'''

Move the mouse
||Now let us scale the '''BezierCurve.'''

Press the '''S''' key and move the mouse. Observe that the curve gets bigger.

When it covers the whole '''3D viewport, '''click to stop the action.

|-
|| Hover over the road and curve
||Let’s now learn to merge both the road and the curve.

|-
|| Select the '''Road'''

Go to '''Properties'''

Click on the spanner shaped icon
||Click on the '''Select box tool. '''Select the '''Road.'''

Go to '''Properties. '''Click on the spanner shaped icon.

This is the '''Modifier Properties.'''

|-
|| Click on '''Add''' and then '''Array'''
||Click on '''Add modifier'''.

A drop down appears.

Go to '''Generate''' and select '''Array.'''

|-
|| Hover on '''Array modifier'''
||Observe '''Array modifier '''opens.

It allows us to create copies of an object and arrange them in a pattern.

|-
|| Change the '''Fit Type''' to '''Fit Curve'''

Select '''BezierCurve'''
||Click on '''Fit Type''' dropdown.'''

Change the''' Fit Type''' to '''Fit Curve.'''

Then click on the '''Curve''' field. Select '''BezierCurve.'''

|-
|| Hover over the '''road'''
||Notice the array pattern on the road is enabled.

But the curve and the road are not yet merged.

|-
|| Click on the '''Add Modifier''' and then on '''Deform'''

Select '''Curve'''

||To do so we will add another '''Modifier'''.

Click on the '''Add Modifier''' and then on '''Deform'''.

From the drop down select '''Curve'''.

|-
|| Click on the Curve''' Object '''field

Select '''BezierCurve'''

||'''Curve modifier''' appears below the '''Array modifier.'''

Click on the '''Curve Object '''field. Select '''BezierCurve.'''

|-
|| Hover over the '''road'''
||Observe the road is merged with the '''BezierCurve''' and appears in a curved shape.

|-
|| Click the mouse wheel and drag the mouse in different directions
||Let's view the road from a different angle.

Hold the mouse wheel and drag the mouse in different directions.

|-
|| Point to the road.
||Let's give some thickness to the road.

|-
|| Go to '''Properties.'''

Click on''' Add Modifier. '''Then on '''Generate. '''

From the drop down select '''Solidify'''

Change the '''Thickness''' to '''0.5'''
||Go to '''Properties. '''Click on''' Add Modifier. '''Then on '''Generate. '''

From the drop down select '''Solidify.'''

'''Solidify '''appears below the''' Curve modifier.'''

Here, change the '''Thickness''' to 0.5.
Press''' Enter.'''

|-
|| Hover over the road
||Notice that the thickness of the road has increased.

|-
|| Click on '''File '''and then '''Save'''

Change the folder name to '''Car-animation. '''

Change the '''untitled.blend''' as '''Road.blend.'''

Click on '''Save blender file'''
||Now the road is created. Let us save the file.

Go to '''File '''and select '''Save'''. Select '''Desktop.'''

You can choose a different location according to your preference.

On the top, click on the folder icon to create a new folder.

Change the folder name to '''Car-animation'''.

In the bottom change the '''untitled.blend''' as '''Road.blend.'''

Click on '''Save blender file.'''

The file is now saved.

We have come to the end of this tutorial.

|-
|| '''Slide Number 5'''

'''Summary '''
||Let’s summarize.

In this tutorial, we have learned to, create a road using the options given here:

* Add and edit a''' plane'''
* Use '''Loop cut'''
* Use '''Viewport Shading modes'''
* Add '''Material''' to an object
* Use '''Array''', '''Curve''' and '''Solidify''' '''modifiers'''

|-
|| '''Slide Number 6'''

'''Assignment '''

||As an assignment, please create a zebra crossing.

* Add a '''plane'''
* Add '''Material''' and change the color to yellow
* Using '''Array modifier '''create a zebra crossing on the road.

|-
|| '''Slide Number 7'''

'''About the Spoken Tutorial Project'''

||The video at the following link summarizes the '''Spoken Tutorial project.'''

Please download and watch it.
|-
|| '''Slide Number 8'''

'''Spoken Tutorial workshops'''

||The '''Spoken Tutorial Project''' team conducts workshops and gives certificates.

For more details, please write to us.
|-
|| '''Slide Number 9'''

'''Answers for THIS Spoken Tutorial'''
|| Please post your timed queries in this '''forum'''.
|-
|| '''Slide Number 10'''

'''FOSSEE Forum'''
|| For any general or technical questions on '''Blender''', visit the '''FOSSEE''' '''forum''' and post your question.
|-
|| '''Slide Number 11'''

'''Acknowledgement'''
||'''The Spoken Tutorial''' project was established by the '''Ministry of Education''', '''Government of India'''.

This is Arthi along with Sejal from '''IIT Bombay''' signing off.

Thanks for joining.
|-
|}

Blender-4.1/C2/Camera-View-Settings/English

2024-08-14T10:04:30Z

Snehalathak:

'''Title''': Camera View Settings

'''Author:''' Pooja Jha & Arthi Varadarajan

'''Keywords''': blender 4.1, camera view, roll, pan, dolly, track, video tutorial.

{| border=1
|-
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Camera view settings '''in''' Blender.'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to:
* Change the location of the camera to get a new camera view
* '''Roll, pan, dolly '''and '''track '''the '''camera view''' and
* Select a new '''camera''' view using the '''fly mode'''.

|-
|| '''Slide Number 3'''

'''Software and System Requirements'''
|| To record this tutorial, I am using

* '''Mac OS version 14.5'''

* '''Blender version 4.1'''

It is recommended to install '''Blender version 4.1 '''or higher.
|-
|| '''Slide Number 4'''

'''Pre-requisites'''
|| To follow this tutorial,
* The learner must be familiar with the '''3D viewport '''in''' blender.'''

|-
|| Cursor on the interface.
|| I have already opened '''Blender'''.

Let us see how to navigate the camera.

|-
|| Hover the cursor on '''User Perspective''',

at the top left corner of '''3D viewport'''.
|| By default, when '''Blender''' opens, the '''3D viewport''' is in the '''User Perspective view'''.
|-
|| Only Narration
|| Now, let’s switch to the''' camera view'''.
|-
|| Click on '''View''' option

'''Camera''' >> '''Active Camera '''

|| Go to the ''' 3D viewport menu bar''' and click on '''View'''.

A menu opens.

Navigate to '''Cameras'''.

From the sub-menu select '''Active Camera'''.
|-
|| Press numpad 0.
|| For keyboard shortcut, press '''numpad 0'''.
|-
|| Hover around the dotted box
|| We can now see the '''camera view'''.

The dotted box around the cube is the field of view of the '''Active camera'''.

All objects inside this box will be rendered.
|-
|| Only Narration
|| '''Blender '''allows us to position the active '''camera'''.

It also allows us to orient the active '''camera''' to match our current view point.

Let’s see how to do this.
|-
|| Video editor:

'''Numpad 0'''
|| Press '''numpad 0 ''' to go back to the '''perspective view'''.

|-
|| Press 0 twice
|| The shortcut '''numpad 0 ''' is a toggle to switch-to and from the '''camera view'''.
|-
|| Hold the mouse wheel.

Move the mouse.
|| Hold the '''mouse wheel''' or the ''' middle mouse button'''.

Then move the '''mouse wheel''' to rotate the camera view.
|-
|| Only Narration
|| This will help us to change the location where we wish to place the '''camera'''.
|-
|| Click on the cube
|| Make sure the '''cube''' is selected.
|-
|| Video editor:

'''Ctrl''', '''Alt''' and '''Numpad 0'''
|| Press '''Ctrl''', '''Alt''' and '''numpad 0''' keys together.
|-
|| Point to the camera.
|| Observe that the '''camera''' moves to the new location.

Also, the '''3D view''' switches to the '''camera view''' at the same time.
|-
|| Only Narration
|| '''Blender''' also allows us to perform a few navigational actions on the '''camera'''.

These are rolling, panning, tracking etc.

We shall now look at these.
|-
|| click on the dotted box.
|| Click on the dotted box to select the '''camera'''.
|-
|| Only Narration
|| Now, we can manipulate the camera like we would manipulate any other object.

Remember that to perform these actions we need to be in the '''camera view'''.
|-
|| Only Narration
|| The first action we shall see is to '''roll ''' the '''camera view'''.
|-
|| Video editor: '''R'''
|| Press '''R '''on your keyboard to enter the object rotation mode.
|-
|| Move your mouse left and right
|| Now move your mouse left to right and up and down.
|-
|| Only Narration
|| By default this rotates the camera in its local '''z-axis'''.

The local '''z-axis''' is an imaginary axis that goes in or out of the camera's view.
|-
|| Video editor: '''Esc'''
|| Right click or press '''Esc ''' on the keyboard to cancel the action.
|-
|| Point to the view.
|| This will take you back to your previous''' camera view.'''
|-
|| Only Narration
|| The next action we shall see is panning the '''camera view'''.
|-
|| Hover left to right and up and down
|| '''Panning''' is in 2 directions – left to right or up and down.
|-
|| Video editor: '''R'''.

Video editor: '''X '''twice
|| Press '''R ''' to enter the object rotation mode.

Press '''X '''twice.
|-
|| Only Narration
|| The first '''X '''locks the rotation to the global x-axis.

The second '''X ''' locks the rotation to the local x-axis.
|-
|| Move the mouse up and down
|| Now move the mouse up and down.
|-
|| Only Narration
|| The '''camera view''' pans up and down.
|-
|| Video editor: '''Y '''twice
|| Press '''Y '''twice.
|-
|| Only Narration
|| The first '''Y '''locks the rotation to the '''global y-axis.'''

The second '''Y '''locks the rotation to the '''local y-axis.'''
|-
|| Move the mouse left to right
|| Now move the mouse left to right.
|-
|| Only Narration
|| The '''camera view''' pans left to right and vice versa.
|-
|| Right click or Press ESc
|| Press '''Esc''' to go back to the''' '''previous''' camera view'''.
|-
|| Only Narration
|| Next we shall '''dolly '''the camera.

|-
|| Only Narration
|| '''Dolly ''' supports moving the view-point to a different place.

It also allows us to transport the view from one place to another.

There are two ways to do this.
|-
|| Video editor: '''G'''

Move the mouse up and down.
|| First press '''G '''on the keyboard.

Then hold the mouse wheel.

Now, move the mouse wheel up and down.

Right click to go back to the '''camera view'''.
|-
|| Only Narration
|| In the second way, you can move the camera along its local '''z-axis'''.
|-
|| Video editor: '''G'''

Video editor: '''Z '''twice

Move the mouse.
|| Press '''G ''' on the keyboard.

Then press '''Z ''' twice to lock the camera to the local '''z- axis'''.

Now, moving the mouse gives the same effect.
|-
|| Right click
|| Right click to go back to the previous '''camera view'''.
|-
|| Only Narration
|| Moving the camera along '''local X''' or '''Y axis''' tracks left-right or up-down motion.
|-
|| Video editor: '''G'''

Video editor: '''X '''twice

Move the mouse left to right.
|| Press '''G'''.

Now press '''X '''twice.

Then move the mouse left to right.
|-
|| Only Narration
|| The '''camera view''' tracks left to right and vice versa.
|-
|| Right click
|| Right click to go back to the previous '''camera view'''.

|-
|| Video editor: '''G'''

Video editor: '''Y '''twice

Move the mouse up and down
|| Now, Press '''G''' and press '''Y '''twice.

Move the mouse up and down.
|-
|| Only Narration
|| The '''camera view ''' tracks up and down.
|-
|| Right click
|| Right click to go back to the previous '''camera view'''.
|-
|| Only Narration
|| '''Blender''' also provides a '''fly mode''' for the camera.
|-
|| Video editor:

'''Shift and Tilde(~)'''
|| Press '''Shift '''and''' Tilde '''keys to enter the '''camera fly mode'''.
|-
|| Only Narration
|| When''' camera fly mode '''is '''ON''' then mouse movement pans the view accordingly.
|-
|| Only Narration
|| Let us now use the keyboard shortcut keys as shown.
|-
|| Video editor: '''W '''
|| Press '''W ''' to zoom into the''' camera view'''.
|-
|| Video editor: '''S '''
|| Press '''S '''to zoom out the '''camera view.'''
|-
|| Video editor: '''A '''
|| On pressing '''A ''' camera is moving to right side.
|-
|| Video editor: '''D '''
||On pressing '''D''', camera is moving to left side.
|-
|| Video editor: '''Q '''
|| Press '''Q''', to shift the '''camera view''' upwards.
|-
|| Video editor: '''E '''
|| Press '''E''', to shift the '''camera view''' downwards.
|-
|| Left click
|| Next, left click on the mouse to lock the''' camera view'''.

|-
|| Only Narration
|| Observe that, now we see the new '''camera view'''.

This brings us to the end of the tutorial.

|-
|| '''Slide Number 5'''

'''Summary '''

|| Let us summarize.

In this tutorial, we have learnt to

* Change the location of the camera to get a new camera view
* Roll, pan, dolly and track the camera view and
* Select a new camera view using the fly mode

|-
|| '''Slide Number 6'''

'''Assignment'''
|| As an assignment, please do the following

* Add a '''cone''' to the right side of the '''cube'''
* Go to camera view
* Go to''' fly mode''' and zoom out the camera view
* Both '''cube''' and '''cone''' should be visible inside the camera view

|-
|| '''Slide Number 7'''

'''About the Spoken Tutorial Project'''
|| The video at the following link summarizes the '''Spoken Tutorial project.'''

Please download and watch it.
|-
|| '''Slide Number 8'''

'''Spoken Tutorial workshops'''
|| The '''Spoken Tutorial Project''' team conducts workshops and gives certificates.

For more details, please write to us.
|-
|| '''Slide Number 9'''

'''Answers for THIS Spoken Tutorial'''
|| Please post your timed queries in this''' forum'''.
|-
|| '''Slide Number 10'''

'''FOSSEE Forum'''
|| For any general or technical questions on '''Blender,''' visit the '''FOSSEE forum '''and post your question.
|-
|| '''Slide Number 11'''

'''Acknowledgement'''
|| '''Spoken Tutorial''' project was established by the '''Ministry of Education''', '''Government of India'''.

|-
||
|| This is Arthi along with Sejal from '''IIT Bombay''' signing off.

Thank you for joining.

|-
|}

AutoDock4/C2/Visualizing-Docking-using-UCSF-Chimera/English

2024-06-19T11:12:44Z

Snehalathak:

'''Title of script''': '''Visualizing Docking using UCSF Chimera'''

'''Author: '''Dr.Snehalatha Kaliappan and Sruthi Sudhakar

'''Keywords: '''Autodock4, docking, UCSF Chimera, receptor, ligand, residues, hydrogen bonds, video tutorial.

{| border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Visualizing Docking using UCSF Chimera'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''

|| In this tutorial, we will,

Open the '''PDB '''file for the receptor on the '''Chimera''' interface.

Select and delete solvent and other residues from the receptor structure.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''

|| Add the most preferred docking pose of the ligand to the receptor structure.

Show hydrogen bonds and other interactions.

|-
|| '''Slide Number 4'''

'''Learning Objectives'''
|| Highlight the active site residues.

Show the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 5'''

'''System Requirement'''

|| Here I am using,

'''Ubuntu Linux ''' OS version 20.04

'''AutoDockTools''' version 1.5.7

'''UCSF Chimera''' version 1.17.2

|-
|| '''Slide Number 6'''

'''Pre-requisites'''

'''https://spoken-tutorial.org/tutorial-search/?search_foss=UCSF+Chimera&search_language=English'''

|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on '''UCSF Chimera''' interface.

Please refer to the link below for tutorials on '''UCSF Chimera''' series.

|-

|| '''Slide number 7'''

'''Code Files'''

||

* The input files required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 8'''

'''Code Files'''

||
* Save the input files in your home directory or working directory

* Make a copy of all the files and then use them for practising.

|-
|| Double-Click on '''Chimera''' icon on the desktop.
|| I will open the '''Chimera''' interface by double-clicking on the shortcut icon on my '''Desktop'''.

'''Chimera''' interface opens.

|-

|| Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

From the '''Open file in the Chimera''' dialog-box, select '''2vta.pdb''' option.

|| Let us load the structure of the receptor on the panel.

Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

'''Open file in Chimera''' dialog-box opens.

From the dialog-box, select '''2vta.pdb''' option.

Click on the '''Open''' button at the bottom.

|-

|| Cursor on the panel.

Click on the Presets menu.

Select '''Interactive 1 (ribbons)''' option.

|| The receptor-ligand complex loads on the panel.

For me the complex opened in ribbons display.

In your case, it may open in a different format.

You can change it to ribbons format using the '''Presets''' menu on the menu bar.

Select '''Interactive 1 (ribbons)''' option to change the display.

|-
|| Cursor on the panel.

Cursor on the ligand.

CELL DIVISION PROTEIN KINASE 2, amino acids 298, chain A

Ligand is small molecule indazole

|| The receptor here is the '''cyclin dependent kinase inhibitor'''.

The ligand is an '''Indazole''' molecule.

|-
|| Cursor on the ligand.
|| We need to delete indazole, glycerol and water molecules from the structure.

|-

|| Click on the '''Select '''menu, from the drop-down select '''Residues '''option.

Cursor on '''GOL, HOH''' and '''LZ1.'''

|| Click on '''Select ''' menu, from the drop-down select '''Residue ''' option.

The sub-menu shows 3 residues under the '''All nonstandard''' category.

'''GOL''', '''HOH ''' and ''' LZ1''', that is, '''glycerol''', water and '''Indazole''' respectively.

|-

|| Click on '''GOL'''.
|| Each time I will select a residue, and delete it.

I will click on''' GOL''' which is glycerol.

|-
|| Cursor on glycerol structure.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Cursor on the panel.

|| Glycerol molecules get highlighted on the panel in green color.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds'''.

From the sub-menu select the '''delete''' option.

Glycerol molecules get deleted from the panel.

|-
|| Click on the '''Select '''menu.

From the drop-down select '''Residues '''option choose HOH/LZ1.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''Delete''' option.

|| Let us delete water molecules and indazole ligand from the structure.

Select water molecules, they are highlighted in green color.

Delete the water molecules from the structure.

Similarly select indazole molecule and delete it.

|-
|| Cursor on the panel.
|| To this receptor structure we will add the best pose conformation of the ligand obtained by '''autodock runs'''.

|-
||Click on the '''File''' menu

select '''Open''', '''Open file in Chimera'''.

dialog-box opens.

Click on the '''File''' menu and select '''Open''', '''Open file in Chimera '''dialog-box opens.

Select '''ligand-conf1.pdb''' from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.
|| From the '''File''' menu, select '''Open''' option.

'''Open file in Chimera '''dialog-box opens.

From the list of files select the '''pdb''' file containing the best pose of the ligand from the '''autodock runs'''.

We had saved this file earlier as '''ligand-conf1.pdb'''.

I will select the file from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|-
|| Cursor on the panel.
|| On the panel you can see the best conformation of the '''indazole''' added to the receptor structure.

|-
|| '''Slide Number 9'''

'''Chimera Tools for Visualization'''.

|| Using tools in '''Chimera''' we can visualize receptor-ligand interactions.

The two kinds of interactions,

* hydrogen bonds and
* other polar and non-polar interactions can be visualized.

We can also visualize the active site pocket and surface properties of the receptor.

|-
|| '''Slide Number 10'''

'''Active Site Residues'''

Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.

|| From the literature, the following residues form much of the ligand binding pocket:

Let us highlight these residues in the structure on the panel.

|-
|| Cursor on the panel.
|| Back to the '''Chimera''' interface.

We will use the command line to select and highlight the active site residues.

|-

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|-

|| Cursor on the '''Command Line''' at the bottom of the interface.
|| Command line panel opens at the bottom of the interface.

Here you can type the commands in the command field to modify the structure.

|-

|| Type,

select :33.A

Press '''Enter'''.

Cursor on the panel.

Click on the '''Actions''' menu on the menu bar.

|| To select Lysine at position 33 on chain A, I will type , '''select space colon 33 dot A'''

Press '''Enter'''.

On the panel you can see the outline highlighted on the cartoon display.

We will display this amino acid as the ball and stick model.

Click on the '''Actions''' menu on the menu bar.

|-
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.
|| Select '''Atoms/Bonds''', choose '''Show ''' from the sub-menu.

Atoms are now displayed as sticks for the '''lysine'''.

|-

|| Click on the '''Actions''' menu on the menu bar.

Select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

|| Click on the '''Actions''' menu again and select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

'''Lysine ''' is now shown as a '''ball and stick '''display.

|-
|| Actions menu again and select the colors option.

Select '''by element''' from the sub menu.

|| Click on the '''Actions''' menu again and select the color option.

Select '''by element''' from the sub menu.

On the panel you can see the '''ball and stick''' model in '''rasmol ''' color coding of elements.

Click on '''Select ''' option and clear the selection.

|-
|| Type,

select: Amino acid code and position number (example Phe 80)

Press Enter.

Click on the Actions >> Atoms/Bonds >> Show

Actions >> Atoms/Bonds >> ball and stick

|| I will show the steps for one more '''AMINO ACID Phenylalanine 80'''.

At the command line edit the command as shown.

Delete the number 33.A

and in its place type 80.A, rest of the command remains as such.

Press '''Enter'''.

|-
|| '''Phenylalanine 80''' is highlighted.
|| '''Phenylalanine 80''' is highlighted.

Go to '''Actions''' menu and click on '''Show'''.

'''Phenylalanine 80''' is shown in sticks display.

Go to '''Actions''', '''Atoms/Bonds''' and click on '''ball & stick'''.

Go to '''Actions''' again select '''color by element'''.

Click on '''Select''' option and clear the selection.

|-
|| Cursor on the panel.
|| Following the same steps, show all the amino acids in the active-site.

Now receptor-ligand complex with the active site amino acids are shown in '''ball and stick''' display.

|-
|| Click on the '''Select''' menu, choose '''Residue''', from the sub menu choose '''LZ1'''.

Cursor on the panel.

|| To view hydrogen bonds formed by ligand and receptor, select the ligand.

Click on the '''Select''' menu,and choose '''Residue''', from the sub menu choose '''LZ1'''.

On the panel, '''LZ1''' is highlighted in green color.

|-
|| Click on the '''Tools '''menu.

Select '''Structure Analysis'''.

From the sub-menu choose''' FindHBond '''option.

|| Click on the '''Tools '''menu.

Select '''Structure Analysis'''.

From the sub-menu choose''' FindHBond''' option.

|-

|| '''H-Bond Parameter''' dialog-box opens.

Click on the check box against '''Label Hydrogen bond with distance'''.

Click on '''Only find H-bonds with at least one end selected.'''

Click on '''Write information to reply log'''.

Click on the '''OK''' button.

|| '''H-Bond Parameters''' dialog-box opens.

In the dialog box,

Fix the color of the '''hydrogen bond''' by clicking the colored box.

I will select yellow color.

Close the Color selection box.

Fix the line width to 3.0 for a thicker line.

* Click on the check box against '''Label Hydrogen bond with distance'''.
* Click on '''Only find H-bonds, with at least one end selected'''.

Uncheck any other check boxes if checked.
* And click on '''Write in formation to reply log'''.

Click on '''Apply''' and '''OK''' buttons.

|-

|| Cursor on the panel.
|| Observe the panel.

'''Hydrogen bonds''' are shown as '''pseudo-bonds''' of specified color and line width.

Here we can see only two hydrogen bonds with '''indazole'''.

|-

|| Click on the''' Favorites''' menu on the menu bar.

From the sub menu select '''Reply log''' option.

|| Details of the bonds can be viewed on the '''Reply log'''.

Open '''Reply log ''' using '''Favorites''' menu.

Click on '''Favorites''' menu.

From the sub menu select '''Reply log''' option.

A pop-up window opens.

Information about each hydrogen bond is given here.

|-

|| Cursor on the '''Reply log '''pop-up information.

Close the pop-up window.

|| One of the bonds, is formed with '''Leucine''' 83 and '''indazole''' nitrogen.

Another is formed with '''Glutamine''' 81 with hydrogen attached to the nitrogen atom of '''indazole'''.

|-

||Cursor on the panel.
||On the panel we can see the hydrogen bond distance.

Close the '''Reply log''' window.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' Findclashes/contacts '''option.

|| There is another feature in the''' Tools''' menu under the '''Structure Analysis''' option.

It is '''Findclashes/contacts'''.

A '''dialog box''' opens.

This feature identifies non-polar interactions such as '''Clashes''' and '''Contacts'''.

|-

|| Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

|| Let us identify '''contacts''' of the '''LZ1''' with all other atoms.

Ligand is already selected on the panel.

Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

It shows '''10 atoms designated.'''

Click on the radio button against “'''All other atoms'''”.

|-

|| Click on the radio button against “'''All other atoms'''”.

Point to '''Include intra-molecule contacts.'''

|| In the '''Clash/Contact Parameters''' section, in the '''Default''' click on the '''Contact''' button.

|-

|| Under '''Treatment of Clash/Contact Atoms,''' click on the following check boxes.

* '''Select'''
* '''Draw pseudo-bonds'''
* '''If endpoint atom hidden'''
* '''And Write information to reply log'''

|| Under '''Treatment of Clash/Contact Atoms,'''

click on the following check boxes.

* '''Select ''' and
* '''Draw pseudo-bonds of color'''.

Click on the color box.

In the '''Color Editor ''' window I will select green.

Close the color selector.

Check the check box for, '''Write information to reply log'''.

|-
|| Click on the '''OK''' button.

Cursor on the panel.

|| Click on the '''OK''' button.

Observe the panel.

All the contacts of ligand''' LZ1 ''' are shown as green lines.

|-
|| Click on the '''Favorites '''menu.

Select '''Reply Log ''' from the sub-menu.

Cursor on the '''Reply Log''' window.

|| Open the '''Reply Log '''using the ''' Favorites ''' menu.

'''Atom-atom contacts''' are listed here.

It shows 21 contacts.

The amino acid residues which made the contact with '''LZ1''' are listed here.

Close the dialog-box.

These residues form the binding site for this receptor-ligand complex.

|-

|| Cursor on the panel.
|| Most of these active site residues are hydrophobic in nature.

Let us create a surface for this complex colored by amino acid '''hydrophobicity'''.

|-

|| Cursor on the panel.
|| Using the '''Presets''' menu let us analyze the hydrophobic surface for this complex.

|-

|| Click on '''Presets''' on the menu bar. From the drop down select '''Interactive 3 hydrophobicity surface'''.

|| Click on '''Presets''' on the menu bar.

From the drop down select '''Interactive 3 hydrophobicity surface'''.

|-

|| Cursor on the panel.
|| The surface represents blue for the most polar residues,

orange for the most hydrophobic,

white for the neutral amino acids.

|-

|| Cursor on the panel.

Rotate and zoom the structure using the mouse.

|| We will rotate and locate the ligand pocket.

As you notice here, most of the ligand binding pocket is '''hydrophobic'''.

|-

|| Click on the''' Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|| The interior of the binding pocket can be viewed using the '''Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|-

|| In the '''Viewing''' window,Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping button'''.

In the pop-up window, check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

Click on '''Close''' button

|| A '''Viewing''' window opens.

You will see a viewing eye and two cutting planes in the '''Viewing''' window.

Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping '''button.

'''Surface Capping''' window opens.

Check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

I will select pink.

Close the color editor.

I will select cap style as solid.

Click on '''Close''' button to close the surface capping window.

|-

|| Change the position of the viewing eye and clipping planes.
|| We can change the position of the viewing eye and clipping planes.

Now we can view the interior of the binding pocket clearly.

You can see clearly that the ligand is attached to the '''hydrophobic pocket'''.

|-
|| '''Slide Number 11'''

'''Conclusion of the Analysis'''
|| Conclusion of the Analysis

The ligand is interacting mostly with the hydrophobic residues inside the binding pocket.

We found many non bonding interactions with the hydrophobic residues.

|-

|| '''Slide Number 12'''

'''Conclusion of the Analysis'''

|| Only a few hydrogen bonds are expected.

We observed only two hydrogen bonds using the '''Structure Analysis tool.'''

|-
|| Cursor on the panel.
|| More hydrophobic groups on the''' indazole '''will increase the interaction and binding with the active site.

We can generate and analyze more conformers to understand the interactions better.

This brings us to the end of this tutorial.

|-

|| '''Slide Number 13'''

'''Summary'''
|| Let us summarize,

In this tutorial, we have,

Opened the PDB file for the receptor on the '''Chimera''' interface.

Selected and deleted solvent and other residues from the receptor structure.

|-
|| '''Slide Number 14'''

'''Summary'''
|| Added the most preferred conformation of the ligand obtained after autodock runs to the receptor structure.

Showed hydrogen bonds and other interactions of the ligand with the receptor.

|-
|| '''Slide Number 15'''

'''Summary'''
|| Highlighted the active site residues.

Showed the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 16'''

'''Assignment'''
|| As an assignment,

Analyze the dlg files generated for '''1DWD''' receptor-ligand complex using '''UCSF Chimera'''.

https://autodock.scripps.edu/download-autodock4/

|-

|| '''Slide Number 17'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 18'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 19'''

'''Forum'''
|| Please post your timed queries in this forum.
|-
|| '''Slide Number 20'''

'''Acknowledgment '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Visualizing-Docking-using-UCSF-Chimera/English

2024-06-19T11:08:38Z

Snehalathak:

'''Title of script''': '''Visualizing Docking using UCSF Chimera'''

'''Author: '''Dr.Snehalatha Kaliappan and Sruthi Sudhakar

'''Keywords: '''Autodock4, docking, UCSF Chimera, receptor, ligand, residues, hydrogen bonds, video tutorial.

{| border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Visualizing Docking using UCSF Chimera'''.

|-
|| '''Slide Number 2'''

'''Learning Objectives'''

|| In this tutorial, we will,

Open the '''PDB '''file for the receptor on the '''Chimera''' interface.

Select and delete solvent and other residues from the receptor structure.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''

|| Add the most preferred docking pose of the ligand to the receptor structure.

Show hydrogen bonds and other interactions.

|-
|| '''Slide Number 4'''

'''Learning Objectives'''
|| Highlight the active site residues.

Show the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 5'''

'''System Requirement'''

|| Here I am using,

'''Ubuntu Linux ''' OS version 20.04

'''AutoDockTools''' version 1.5.7

'''UCSF Chimera''' version 1.17.2

|-
|| '''Slide Number 6'''

'''Pre-requisites'''

'''https://spoken-tutorial.org/tutorial-search/?search_foss=UCSF+Chimera&search_language=English'''

|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on '''UCSF Chimera''' interface.

Please refer to the link below for tutorials on '''UCSF Chimera''' series.

|-

|| '''Slide number 7'''

'''Code Files'''

||

* The input files required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 8'''

'''Code Files'''

||
* Save the input files in your home directory or working directory

* Make a copy of all the files and then use them for practising.

|-
|| Double-Click on '''Chimera''' icon on the desktop.
|| I will open the '''Chimera''' interface by double-clicking on the shortcut icon on my '''Desktop'''.

'''Chimera''' interface opens.

|-

|| Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

From the '''Open file in the Chimera''' dialog-box, select '''2vta.pdb''' option.

|| Let us load the structure of the receptor on the panel.

Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

'''Open file in Chimera''' dialog-box opens.

From the dialog-box, select '''2vta.pdb''' option.

Click on the '''Open''' button at the bottom.

|-

|| Cursor on the panel.

Click on the Presets menu.

Select '''Interactive 1 (ribbons)''' option.

|| The receptor-ligand complex loads on the panel.

For me the complex opened in ribbons display.

In your case, it may open in a different format.

You can change it to ribbons format using the '''Presets''' menu on the menu bar.

Select '''Interactive 1 (ribbons)''' option to change the display.

|-
|| Cursor on the panel.

Cursor on the ligand.

CELL DIVISION PROTEIN KINASE 2, amino acids 298, chain A

Ligand is small molecule indazole

|| The receptor here is the '''cyclin dependent kinase inhibitor'''.

The ligand is an '''Indazole''' molecule.

|-
|| Cursor on the ligand.
|| We need to delete indazole, glycerol and water molecules from the structure.

|-

|| Click on the '''Select '''menu, from the drop-down select '''Residues '''option.

Cursor on '''GOL, HOH''' and '''LZ1.'''

|| Click on '''Select ''' menu, from the drop-down select '''Residue ''' option.

The sub-menu shows 3 residues under the '''All nonstandard''' category.

'''GOL''', '''HOH ''' and ''' LZ1''', that is, '''glycerol''', water and '''Indazole''' respectively.

|-

|| Click on '''GOL'''.
|| Each time I will select a residue, and delete it.

I will click on''' GOL''' which is glycerol.

|-
|| Cursor on glycerol structure.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Cursor on the panel.

|| Glycerol molecules get highlighted on the panel in green color.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds'''.

From the sub-menu select the '''delete''' option.

Glycerol molecules get deleted from the panel.

|-
|| Click on the '''Select '''menu.

From the drop-down select '''Residues '''option choose HOH/LZ1.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''Delete''' option.

|| Let us delete water molecules and indazole ligand from the structure.

Select water molecules, they are highlighted in green color.

Delete the water molecules from the structure.

Similarly select indazole molecule and delete it.

|-
|| Cursor on the panel.
|| To this receptor structure we will add the best pose conformation of the ligand obtained by '''autodock runs'''.

|-
||Click on the '''File''' menu

select '''Open''', '''Open file in Chimera'''.

dialog-box opens.

Click on the '''File''' menu and select '''Open''', '''Open file in Chimera '''dialog-box opens.

Select '''ligand-conf1.pdb''' from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.
|| From the '''File''' menu, select '''Open''' option.

'''Open file in Chimera '''dialog-box opens.

From the list of files select the '''pdb''' file containing the best pose of the ligand from the '''autodock runs'''.

We had saved this file earlier as '''ligand-conf1.pdb'''.

I will select the file from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|-
|| Cursor on the panel.
|| On the panel you can see the best conformation of the '''indazole''' added to the receptor structure.

|-
|| '''Slide Number 9'''

'''Chimera Tools for Visualization'''.

|| Using tools in '''Chimera''' we can visualize receptor-ligand interactions.

The two kinds of interactions,

* hydrogen bonds and
* other polar and non-polar interactions can be visualized.

We can also visualize the active site pocket and surface properties of the receptor.

|-
|| '''Slide Number 10'''

'''Active Site Residues'''

Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.

|| From the literature, the following residues form much of the ligand binding pocket:

Let us highlight these residues in the structure on the panel.

|-
|| Cursor on the panel.
|| Back to the '''Chimera''' interface.

We will use the command line to select and highlight the active site residues.

|-

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|-

|| Cursor on the '''Command Line''' at the bottom of the interface.
|| Command line panel opens at the bottom of the interface.

Here you can type the commands in the command field to modify the structure.

|-

|| Type,

select :33.A

Press '''Enter'''.

Cursor on the panel.

Click on the '''Actions''' menu on the menu bar.

|| To select Lysine at position 33 on chain A, I will type , '''select space colon 33 dot A'''

Press '''Enter'''.

On the panel you can see the outline highlighted on the cartoon display.

We will display this amino acid as the ball and stick model.

Click on the '''Actions''' menu on the menu bar.

|-
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.
|| Select '''Atoms/Bonds''', choose '''Show ''' from the sub-menu.

Atoms are now displayed as sticks for the '''lysine'''.

|-

|| Click on the '''Actions''' menu on the menu bar.

Select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

|| Click on the '''Actions''' menu again and select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

'''Lysine ''' is now shown as a '''ball and stick '''display.

|-
|| Actions menu again and select the colors option.

Select '''by element''' from the sub menu.

|| Click on the '''Actions''' menu again and select the color option.

Select '''by element''' from the sub menu.

On the panel you can see the '''ball and stick''' model in '''rasmol ''' color coding of elements.

Click on '''Select ''' option and clear the selection.

|-
|| Type,

select: Amino acid code and position number (example Phe 80)

Press Enter.

Click on the Actions >> Atoms/Bonds >> Show

Actions >> Atoms/Bonds >> ball and stick

|| I will show the steps for one more '''AMINO ACID Phenylalanine 80'''.

At the command line edit the command as shown.

Delete the number 33.A

and in its place type 80.A, rest of the command remains as such.

Press '''Enter'''.

|-
|| '''Phenylalanine 80''' is highlighted.
|| '''Phenylalanine 80''' is highlighted.

Go to '''Actions''' menu and click on '''Show'''.

'''Phenylalanine 80''' is shown in sticks display.

Go to '''Actions''', '''Atoms/Bonds''' and click on '''ball & stick'''.

Go to '''Actions''' again select '''color by element'''.

Click on '''Select''' option and clear the selection.

|-
|| Cursor on the panel.
|| Following the same steps, show all the amino acids in the active-site.

Now receptor-ligand complex with the active site amino acids are shown in '''ball and stick''' display.

|-
|| Click on the '''Select''' menu, choose '''Residue''', from the sub menu choose '''LZ1'''.

Cursor on the panel.

|| To view hydrogen bonds formed by ligand and receptor, select the ligand.

Click on the '''Select''' menu,and choose '''Residue''', from the sub menu choose '''LZ1'''.

On the panel, '''LZ1''' is highlighted in green color.

|-
|| Click on the '''Tools '''menu.

Select '''Structure Analysis'''.

From the sub-menu choose''' FindHBond '''option.

|| Click on the '''Tools '''menu.

Select '''Structure Analysis'''.

From the sub-menu choose''' FindHBond''' option.

|-

|| '''H-Bond Parameter''' dialog-box opens.

Click on the check box against '''Label Hydrogen bond with distance'''.

Click on '''Only find H-bonds with at least one end selected.'''

Click on '''Write information to reply log'''.

Click on the '''OK''' button.

|| '''H-Bond Parameters''' dialog-box opens.

In the dialog box,

Fix the color of the '''hydrogen bond''' by clicking the colored box.

I will select yellow color.

Close the Color selection box.

Fix the line width to 3.0 for a thicker line.

* Click on the check box against '''Label Hydrogen bond with distance'''.
* Click on '''Only find H-bonds, with at least one end selected'''.

Uncheck any other check boxes if checked.
* And click on '''Write in formation to reply log'''.

Click on '''Apply''' and '''OK''' buttons.

|-

|| Cursor on the panel.
|| Observe the panel.

'''Hydrogen bonds''' are shown as '''pseudo-bonds''' of specified color and line width.

Here we can see only two hydrogen bonds with '''indazole'''.

|-

|| Click on the''' Favorites''' menu on the menu bar.

From the sub menu select '''Reply log''' option.

|| Details of the bonds can be viewed on the '''Reply log'''.

Open '''Reply log ''' using '''Favorites''' menu.

Click on '''Favorites''' menu.

From the sub menu select '''Reply log''' option.

A pop-up window opens.

Information about each hydrogen bond is given here.

|-

|| Cursor on the '''Reply log '''pop-up information.

Close the pop-up window.

|| One of the bonds, is formed with '''Leucine''' 83 and '''indazole''' nitrogen.

Another is formed with '''Glutamine''' 81 with hydrogen attached to the nitrogen atom of '''indazole'''.

|-

||Cursor on the panel.
||On the panel we can see the hydrogen bond distance.

Close the '''Reply log''' window.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' Findclashes/contacts '''option.

|| There is another feature in the''' Tools''' menu under the '''Structure Analysis''' option.

It is '''Findclashes/contacts'''.

A '''dialog box''' opens.

This feature identifies non-polar interactions such as '''Clashes''' and '''Contacts'''.

|-

|| Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

|| Let us identify '''contacts''' of the '''LZ1''' with all other atoms.

Ligand is already selected on the panel.

Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

It shows '''10 atoms designated.'''

Click on the radio button against “'''All other atoms'''”.

|-

|| Click on the radio button against “'''All other atoms'''”.

Point to '''Include intra-molecule contacts.'''

|| In the '''Clash/Contact Parameters''' section, in the '''Default''' click on the '''Contact''' button.

|-

|| Under '''Treatment of Clash/Contact Atoms,''' click on the following check boxes.

* '''Select'''
* '''Draw pseudo-bonds'''
* '''If endpoint atom hidden'''
* '''And Write information to reply log'''

|| Under '''Treatment of Clash/Contact Atoms,'''

click on the following check boxes.

* '''Select ''' and
* '''Draw pseudo-bonds of color'''.

Click on the color box.

In the '''Color Editor ''' window I will select green.

Close the color selector.

Check the check box for, '''Write information to reply log'''.

|-
|| Click on the '''OK''' button.

Cursor on the panel.

|| Click on the '''OK''' button.

Observe the panel.

All the contacts of ligand''' LZ1 ''' are shown as green lines.

|-
|| Click on the '''Favorites '''menu.

Select '''Reply Log ''' from the sub-menu.

Cursor on the '''Reply Log''' window.

|| Open the '''Reply Log '''using the ''' Favorites ''' menu.

'''Atom-atom contacts''' are listed here.

It shows 21 contacts.

The amino acid residues which made the contact with '''LZ1''' are listed here.

Close the dialog-box.

These residues form the binding site for this receptor-ligand complex.

|-

|| Cursor on the panel.
|| Most of these active site residues are hydrophobic in nature.

Let us create a surface for this complex colored by amino acid '''hydrophobicity'''.

|-

|| Cursor on the panel.
|| Using the '''Presets''' menu let us analyze the hydrophobic surface for this complex.

|-

|| Click on '''Presets''' on the menu bar. From the drop down select '''Interactive 3 hydrophobicity surface'''.

|| Click on '''Presets''' on the menu bar.

From the drop down select '''Interactive 3 hydrophobicity surface'''.

|-

|| Cursor on the panel.
|| The surface represents blue for the most polar residues,

orange for the most hydrophobic,

white for the neutral amino acids.

|-

|| Cursor on the panel.

Rotate and zoom the structure using the mouse.

|| We will rotate and locate the ligand pocket.

As you notice here, most of the ligand binding pocket is '''hydrophobic'''.

|-

|| Click on the''' Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|| The interior of the binding pocket can be viewed using the '''Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|-

|| In the '''Viewing''' window,Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping button'''.

In the pop-up window, check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

Click on '''Close''' button

|| A '''Viewing''' window opens.

You will see a viewing eye and two cutting planes in the '''Viewing''' window.

Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping '''button.

'''Surface Capping''' window opens.

Check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

I will select pink.

Close the color editor.

I will select cap style as solid.

Click on '''Close''' button to close the surface capping window.

|-

|| Change the position of the viewing eye and clipping planes.
|| We can change the position of the viewing eye and clipping planes.

Now we can view the interior of the binding pocket clearly.

You can see clearly that the ligand is attached to the '''hydrophobic pocket'''.

|-
|| '''Slide Number 11'''

'''Conclusion of the Analysis'''
|| Conclusion of the Analysis

The ligand is interacting mostly with the hydrophobic residues inside the binding pocket.

We found many non bonding interactions with the hydrophobic residues.

|-

|| '''Slide Number 12'''

'''Conclusion of the Analysis'''

|| Only a few hydrogen bonds a re expected.

We observed only two hydrogen bonds using the '''Structure Analysis tool.'''

|-
|| Cursor on the panel.
|| More hydrophobic groups on the''' indazole '''will increase the interaction and binding with the active site.

We can generate and analyze more conformers to understand the interactions better.

This brings us to the end of this tutorial.

|-

|| '''Slide Number 13'''

'''Summary'''
|| Let us summarize,

In this tutorial, we have,

Opened the PDB file for the receptor on the '''Chimera''' interface.

Selected and deleted solvent and other residues from the receptor structure.

|-
|| '''Slide Number 14'''

'''Summary'''
|| Added the most preferred conformation of the ligand obtained after autodock runs to the receptor structure.

Showed hydrogen bonds and other interactions of the ligand with the receptor.

|-
|| '''Slide Number 15'''

'''Summary'''
|| Highlighted the active site residues.

Showed the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 16'''

'''Assignment'''
|| As an assignment,

Analyze the dlg files generated for '''1DWD''' receptor-ligand complex using '''UCSF Chimera'''.

https://autodock.scripps.edu/download-autodock4/

|-

|| '''Slide Number 17'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 18'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 19'''

'''Forum'''
|| Please post your timed queries in this forum.
|-
|| '''Slide Number 20'''

'''Acknowledgment '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Visualizing-Docking-using-UCSF-Chimera/English

2024-06-18T09:11:35Z

Snehalathak:

'''Title of script''': '''Visualizing Docking using UCSF Chimera'''

'''Author: '''Dr.Snehalatha Kaliappan and Sruthi Sudhakar

'''Keywords: '''Autodock4, docking, UCSF Chimera, receptor, ligand, residues, hydrogen bonds, video tutorial.

{| border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Visualizing Docking using UCSF Chimera.'''

|-
|| '''Slide Number 2'''

'''Learning Objectives'''

|| In this tutorial, we will,

Open the '''PDB '''file for the receptor on the '''Chimera''' interface.

Select and delete solvent and other residues from the receptor structure.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''

|| Add the most preferred docking pose of the ligand to the receptor structure.

Show hydrogen bonds and other interactions.

|-
|| '''Slide Number 4'''

'''Learning Objectives'''
|| Highlight the active site residues.

Show the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 5'''

'''System Requirement'''

|| Here I am using,

'''Ubuntu Linux '''OS version 20.04

AutoDockTools version 1.5.7

UCSF Chimera version 1.17.2

|-
|| '''Slide Number 6'''

'''Pre-requisites'''

'''https://spoken-tutorial.org/tutorial-search/?search_foss=UCSF+Chimera&search_language=English'''

|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on UCSF Chimera interface.

Please refer to the link below for tutorials on UCSF Chimera series.

|-

|| '''Slide number 7'''

'''Code Files'''

||

* The input files required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 8'''

'''Code Files'''

||
* Save the input files in your home directory or working directory

* Make a copy of all the files and then use them for practising.

|-
|| Double-Click on '''Chimera''' icon on the desktop.
|| I will open the '''Chimera''' interface by double-clicking on the shortcut icon on my '''Desktop'''.

'''Chimera''' interface opens.

|-

|| Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

From the '''Open file in the Chimera''' dialog-box, select '''2vta.pdb''' option.

|| Let us load the structure of the receptor on the panel.

Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

'''Open file in Chimera''' dialog-box opens.

From the dialog-box, select '''2vta.pdb''' option.

Click on the '''Open''' button at the bottom.

|-

|| Cursor on the panel.

Click on the Presets menu.

Select '''Interactive 1 (ribbons)''' option.

|| The receptor-ligand complex loads on the panel.

For me the complex opened in ribbons display.

In your case, it may open in a different format.

You can change it to ribbons format using the '''Presets''' menu on the menu bar.

Select '''Interactive 1 (ribbons)''' option to change the display.

|-
|| Cursor on the panel.

Cursor on the ligand.

CELL DIVISION PROTEIN KINASE 2, amino acids 298, chain A

Ligand is small molecule indazole

|| The receptor here is the '''cyclin dependent kinase inhibitor'''.

The ligand is an '''Indazole''' molecule.

|-
|| Cursor on the ligand.
|| We need to delete indazole, glycerol and water molecules from the structure.

|-

|| Click on the '''Select '''menu, from the drop-down select '''Residues '''option.

Cursor on '''GOL, HOH''' and '''LZ1.'''

|| Click on '''Select '''menu, from the drop-down select '''Residue '''option.

The sub-menu shows 3 residues under the A'''ll nonstandard''' category.

'''GOL, HOH '''and''' LZ1''', that is, '''glycerol''', water and '''Indazole''' respectively.

|-

|| Click on '''GOL'''.
|| Each time I will select a residue, and delete it.

I will click on''' GOL''' which is glycerol.

|-

|| Cursor on glycerol structure.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Cursor on the panel.

|| Glycerol molecules get highlighted on the panel in green color.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Glycerol molecules get deleted from the panel.

|-

|| Click on the '''Select '''menu.

From the drop-down select '''Residues '''option choose HOH/LZ1.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''Delete''' option.

|| Let us delete water molecules and indazole ligand from the structure.

Select water molecules, they are highlighted in green color.

Delete the water molecules from the structure.

Similarly select indazole molecule and delete it.

|-

|| Cursor on the panel.
|| To this receptor structure we will add the best pose conformation of the ligand obtained by '''autodock runs'''.

|-
||Click on the '''File''' menu

select '''Open''', '''Open file in Chimera'''.

dialog-box opens.

Click on the '''File''' menu and select '''Open''', '''Open file in Chimera '''dialog-box opens.

Select '''ligand-conf1.pdb''' from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|| From the '''File''' menu, select '''Open''' option.

'''Open file in Chimera '''dialog-box opens.

From the list of files select the '''pdb''' file containing the best pose of the ligand from the '''autodock runs'''.

We had saved this file earlier as '''ligand-conf1.pdb.'''

I will select the file from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|-
|| Cursor on the panel.
|| On the panel you can see the best conformation of the '''indazole''' added to the receptor structure.

|-

|| '''Slide Number 9'''

'''Chimera Tools for Visualization'''.

|| Using tools in '''Chimera''' we can visualize receptor-ligand interactions.

The two kinds of interactions,

* hydrogen bonds and
* other polar and no n-polar interactions can be visualized.

We can also visualize the active site pocket and surface properties of the receptor.

|-
|| '''Slide Number 10'''

'''Active Site Residues'''

|| From the literature, the following residues form much of the ligand binding pocket:

Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.

Let us highlight these residues in the structure on the panel.

|-
|| Cursor on the panel.
|| Back to the '''Chimera''' interface.

We will use the command line to select and highlight the active site residues.

|-

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|-

|| Cursor on the '''Command Line''' at the bottom of the interface.
|| Command line panel opens at the bottom of the interface.

Here you can type the commands in the command field to modify the structure.

|-

|| Type,

select :33.A

Press '''Enter'''.

Cursor on the panel.

Click on the '''Actions''' menu on the menu bar.

|| To select Lysine at position 33 on chain A, I will type , '''select space colon 33 dot A'''

Press '''Enter'''.

On the panel you can see the outline highlighted on the cartoon display.

We will display this amino acid as the ball and stick model.

Click on the '''Actions''' menu on the menu bar.

|-

|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.

Atoms are now displayed as sticks for the '''lysine'''.

|-

|| Click on the '''Actions''' menu on the menu bar.

Select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

|| Click on the '''Actions''' menu again and select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

'''Lysine ''' is now shown as a '''ball and stick '''display.

|-

|| Actions menu again and select the colors option.

Select '''by element''' from the sub menu.

|| Click on the '''Actions''' menu again and select the color option.

Select '''by element''' from the sub menu.

On the panel you can see the '''ball and stick''' model in '''rasmol '''color coding of elements.

Click on '''Select '''option and clear the selection.

|-
|| Type,

select: Amino acid code and position number (example Phe 80)

Press Enter.

Click on the Actions >> Atoms/Bonds >> Show

Actions >> Atoms/Bonds >> ball and stick

|| I will show the steps for one more '''AMINO ACID Phenylalanine 80'''.

At the command line edit the command as shown.

Delete number 33.A

and in its place type 80.A, rest of the command remains as such.

Press '''Enter'''.

|-
|| '''Phenylalanine 80''' is highlighted.
|| '''Phenylalanine 80''' is highlighted.

Go to '''Actions''' menu and click on '''Show''', '''Phenylalanine 80''' is shown in sticks display.

Go to '''Actions''', '''Atoms/Bonds''' and click on '''ball & stick'''.

Go to '''Actions''' again select '''color by element'''.

Click on '''Select''' option and clear the selection.

|-
|| Cursor on the panel.
|| Following the same steps, show all the amino acids in the active-site.

Now receptor-ligand complex with the active site amino acids are shown in '''ball and stick''' display.

|-
|| Click on the '''Select''' menu, choose '''Residue''', from the sub menu choose '''LZ1'''.

Cursor on the panel.

|| To view hydrogen bonds formed by ligand and receptor, select the ligand.

Click on the '''Select''' menu,and choose '''Residue''', from the sub menu choose '''LZ1'''.

On the panel, '''LZ1''' is highlighted in green color.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' FindHBond '''option.

|| Click on the '''Tools '''menu.

Select '''Structure Analysis, '''from the sub-menu choose''' FindHBond '''option.

|-

|| '''H-Bond Parameter''' dialog-box opens.

Click on the check box against '''Label Hydrogen bond with distance'''.

Click on '''Only find H-bonds with at least one end selected.'''

Click on '''Write information to reply log'''.

Click on the '''OK''' button.

|| '''H-Bond Parameters''' dialog-box opens.

In the dialog box,

Fix the color of the '''hydrogen bond''' by clicking the colored box.

I will select yellow color.

Close the Color selection box.

Fix the line width to 3.0 for a thicker line.

* Click on the check box against '''Label Hydrogen bond with distance'''.
* Click on '''Only find H-bonds, with at least one end selected.'''

Uncheck any other check boxes if checked.* And click on '''Write in formation to reply log'''.

Click on '''Apply''' and '''OK''' buttons.

|-

|| Cursor on the panel.
|| Observe the panel.

'''Hydrogen bonds''' are shown as '''pseudo'''-bonds of specified color and line width.

Here we can see only two hydrogen bonds with '''indazole'''.

|-

|| Click on the''' Favorites''' menu on the menu bar.

From the sub menu select '''Reply log''' option.

|| Details of the bonds can be viewed on the '''Reply log'''.

Open '''Reply log '''using '''Favorites''' menu.

Click on '''Favorites''' menu.

From the sub menu select '''Reply log''' option.

A pop-up window opens.

Information about each hydrogen bond is given here.

|-

|| Cursor on the '''Reply log '''pop-up information.

Close the pop-up window.

|| One of the bonds, is formed with '''Leucine''' 83 and '''indazole''' nitrogen.

Another is formed with '''Glutamine''' 81 with hydrogen attached to the nitrogen atom of '''indazole'''.

|-

||Cursor on the panel.
|| On the panel we can see the hydrogen bond distance.

Close the '''Reply log''' window.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' Findclashes/contacts '''option.

|| There is another feature in the''' Tools''' menu under the '''Structure Analysis''' option.

It is '''Findclashes/contacts'''.

A '''dialog box''' opens.

This feature identifies non-polar interactions such as '''Clashes''' and '''Contacts'''.

|-

|| Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

|| Let us identify '''contacts''' of the '''LZ1''' with all other atoms.

Ligand is already selected on the panel.

Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

It shows '''10 atoms designated.'''

Click on the radio button against “'''All other atoms'''”.

|-

|| Click on the radio button against “'''All other atoms'''”.

Point to '''Include intra-molecule contacts.'''

|| In the '''Clash/Contact Parameters''' section, in the '''Default''' click on the '''Contact''' button.

|-

|| Under '''Treatment of Clash/Contact Atoms,''' click on the following check boxes.

* '''Select'''
* '''Draw pseudo-bonds'''
* '''If endpoint atom hidden'''
* '''And Write information to reply log'''

|| Under '''Treatment of Clash/Contact Atoms,'''

click on the following check boxes.

* '''Select ''' and
* '''Draw pseudo-bonds of color'''.

Click on the color box.

In the '''Color Editor '''window I will select green.

Close the color selector.

Check the check box for, '''Write information to reply log'''.

|-
|| Click on the '''OK''' button.

Cursor on the panel.

|| Click on the '''OK''' button.

Observe the panel.

All the contacts of ligand''' LZ1 '''are shown as green lines.

|-
|| Click on the '''Favorites '''menu.

Select '''Reply Log ''' from the sub-menu.

Cursor on the '''Reply Log''' window.

|| Open the '''Reply Log '''using the ''' Favorites ''' menu.

'''Atom-atom contacts''' are listed here.

It shows 21 contacts.

The amino acid residues which made the contact with '''LZ1''' are listed here.

Close the dialog-box.

These residues form the binding site for this receptor-ligand complex.

|-

|| Cursor on the panel.
|| Most of these active site residues are hydrophobic in nature.

Let us create a surface for this complex colored by amino acid '''hydrophobicity'''.

|-

|| Cursor on the panel.
|| Using the '''Presets''' menu let us analyze the hydrophobic surface for this complex.

|-

|| Click on '''Presets''' on the menu bar. From the drop down select '''Interactive 3 hydrophobicity surface'''.

|| Click on '''Presets''' on the menu bar.

From the drop down select '''Interactive 3 hydrophobicity surface'''.

|-

|| Cursor on the panel.
|| The surface represents blue for the most polar residues,

orange for the most hydrophobic,

white for the neutral amino acids.

|-

|| Cursor on the panel.

Rotate and zoom the structure using the mouse.

|| We will rotate and locate the ligand pocket.

As you notice here, most of the ligand binding pocket is '''hydrophobic'''.

|-

|| Click on the''' Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|| The interior of the binding pocket can be viewed using the '''Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|-

|| In the '''Viewing''' window,Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping button'''.

In the pop-up window, check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

Click on '''Close''' button

|| A '''Viewing''' window opens.

You will see a viewing eye and two cutting planes in the '''Viewing''' window.

Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping '''button.

'''Surface Capping''' window opens.

Check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

I will select pink.

Close the color editor.

I will select cap style as solid.

Click on '''Close''' button to close the surface capping window.

|-

|| Change the position of the viewing eye and clipping planes.
|| We can change the position of the viewing eye and clipping planes.

Now we can view the interior of the binding pocket clearly.

You can see clearly that the ligand is attached to the '''hydrophobic pocket'''.

|-
|| '''Slide Number 11'''

'''Conclusion of the Analysis'''
|| Conclusion of the Analysis

The ligand is interacting mostly with the hydrophobic residues inside the binding pocket.

We found many non bonding interactions with the hydrophobic residues.

|-

|| '''Slide Number 12'''

'''Conclusion of the Analysis'''

|| Only a few hydrogen bonds a re expected.

We observed only two hydrogen bonds using the '''Structure Analysis tool.'''

|-
|| Cursor on the panel.
|| More hydrophobic groups on the''' indazole '''will increase the interaction and binding with the active site.

We can generate and analyze more conformers to understand the interactions better.

This brings us to the end of this tutorial.

|-

|| '''Slide Number 13'''

'''Summary'''
|| Let us summarize,

In this tutorial, we have,

Opened the PDB file for the receptor on the '''Chimera''' interface.

Selected and deleted solvent and other residues from the receptor structure.

|-
|| '''Slide Number 14'''

'''Summary'''
|| Added the most preferred conformation of the ligand obtained after autodock runs to the receptor structure.

Showed hydrogen bonds and other interactions of the ligand with the receptor.

|-
|| '''Slide Number 15'''

'''Summary'''
|| Highlighted the active site residues.

Showed the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 16'''

'''Assignment'''
|| As an assignment,

Analyze the dlg files generated for '''1DWD''' receptor-ligand complex using '''UCSF Chimera'''.

https://autodock.scripps.edu/download-autodock4/

|-

|| '''Slide Number 17'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 18'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 19'''

'''Forum'''
|| Please post your timed queries in this forum.
|-
|| '''Slide Number 20'''

'''Acknowledgment '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Visualizing-Docking-using-UCSF-Chimera/English

2024-06-18T09:07:36Z

Snehalathak:

'''Title of script''': '''Visualizing Docking using UCSF Chimera'''

'''Author: '''Dr.Snehalatha Kaliappan and Sruthi Sudhakar

'''Keywords: '''Autodock4, docking, UCSF Chimera, receptor, ligand, residues, hydrogen bonds, video tutorial.

{| border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Visualizing Docking using UCSF Chimera.'''

|-
|| '''Slide Number 2'''

'''Learning Objectives'''

|| In this tutorial, we will,

Open the '''PDB '''file for the receptor on the '''Chimera''' interface.

Select and delete solvent and other residues from the receptor structure.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''

|| Add the most preferred docking pose of the ligand to the receptor structure.

Show hydrogen bonds and other interactions.

|-
|| '''Slide Number 4'''

'''Learning Objectives'''
|| Highlight the active site residues.

Show the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 5'''

'''System Requirement'''

|| Here I am using,

'''Ubuntu Linux '''OS version 20.04

AutoDockTools version 1.5.7

UCSF Chimera version 1.17.2

|-
|| '''Slide Number 6'''

'''Pre-requisites'''

'''https://spoken-tutorial.org/tutorial-search/?search_foss=UCSF+Chimera&search_language=English'''

|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on UCSF Chimera interface.

Please refer to the link below for tutorials on UCSF Chimera series.

|-

|| '''Slide number 7'''

'''Code Files'''

||

* The input files required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 8'''

'''Code Files'''

||
* Save the input files in your home directory or working directory

* Make a copy of all the files and then use them for practising.

|-
|| Double-Click on '''Chimera''' icon on the desktop.
|| I will open the '''Chimera''' interface by double-clicking on the shortcut icon on my '''Desktop'''.

'''Chimera''' interface opens.

|-

|| Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

From the '''Open file in the Chimera''' dialog-box, select '''2vta.pdb''' option.

|| Let us load the structure of the receptor on the panel.

Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

'''Open file in Chimera''' dialog-box opens.

From the dialog-box, select '''2vta.pdb''' option.

Click on the '''Open''' button at the bottom.

|-

|| Cursor on the panel.

Click on the Presets menu.

Select '''Interactive 1 (ribbons)''' option.

|| The receptor-ligand complex loads on the panel.

For me the complex opened in ribbons display.

In your case, it may open in a different format.

You can change it to ribbons format using the '''Presets''' menu on the menu bar.

Select '''Interactive 1 (ribbons)''' option to change the display.

|-
|| Cursor on the panel.

Cursor on the ligand.

CELL DIVISION PROTEIN KINASE 2, amino acids 298, chain A

Ligand is small molecule indazole

|| The receptor here is the '''cyclin dependent kinase inhibitor'''.

The ligand is an '''Indazole''' molecule.

|-
|| Cursor on the ligand.
|| We need to delete indazole, glycerol and water molecules from the structure.

|-

|| Click on the '''Select '''menu, from the drop-down select '''Residues '''option.

Cursor on '''GOL, HOH''' and '''LZ1.'''

|| Click on '''Select '''menu, from the drop-down select '''Residue '''option.

The sub-menu shows 3 residues under the A'''ll nonstandard''' category.

'''GOL, HOH '''and''' LZ1''', that is, '''glycerol''', water and '''Indazole''' respectively.

|-

|| Click on '''GOL'''.
|| Each time I will select a residue, and delete it.

I will click on''' GOL''' which is glycerol.

|-

|| Cursor on glycerol structure.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Cursor on the panel.

|| Glycerol molecules get highlighted on the panel in green color.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Glycerol molecules get deleted from the panel.

|-

|| Click on the '''Select '''menu.

From the drop-down select '''Residues '''option choose HOH/LZ1.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''Delete''' option.

|| Let us delete water molecules and indazole ligand from the structure.

Select water molecules, they are highlighted in green color.

Delete the water molecules from the structure.

Similarly select indazole molecule and delete it.

|-

|| Cursor on the panel.
|| To this receptor structure we will add the best pose conformation of the ligand obtained by '''autodock runs'''.

|-
||Click on the '''File''' menu

select '''Open''', '''Open file in Chimera'''.

dialog-box opens.
|| Click on the '''File''' menu and select '''Open''', '''Open file in Chimera '''dialog-box opens.

Select '''ligand-conf1.pdb''' from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|| From the '''File''' menu, select '''Open''' option.

'''Open file in Chimera '''dialog-box opens.

From the list of files select the '''pdb''' file containing the best pose of the ligand from the '''autodock runs'''.

We had saved this file earlier as '''ligand-conf1.pdb.'''

I will select the file from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|-
|| Cursor on the panel.
|| On the panel you can see the best conformation of the '''indazole''' added to the receptor structure.

|-

|| '''Slide Number 9'''

'''Chimera Tools for Visualization'''.

|| Using tools in '''Chimera''' we can visualize receptor-ligand interactions.

The two kinds of interactions,

* hydrogen bonds and
* other polar and no n-polar interactions can be visualized.

We can also visualize the active site pocket and surface properties of the receptor.

|-
|| '''Slide Number 10'''

'''Active Site Residues'''

|| From the literature, the following residues form much of the ligand binding pocket:

Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.

Let us highlight these residues in the structure on the panel.

|-
|| Cursor on the panel.
|| Back to the '''Chimera''' interface.

We will use the command line to select and highlight the active site residues.

|-

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|-

|| Cursor on the '''Command Line''' at the bottom of the interface.
|| Command line panel opens at the bottom of the interface.

Here you can type the commands in the command field to modify the structure.

|-

|| Type,

select :33.A

Press '''Enter'''.

Cursor on the panel.

Click on the '''Actions''' menu on the menu bar.

|| To select Lysine at position 33 on chain A, I will type , '''select space colon 33 dot A'''

Press '''Enter'''.

On the panel you can see the outline highlighted on the cartoon display.

We will display this amino acid as the ball and stick model.

Click on the '''Actions''' menu on the menu bar.

|-

|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.

Atoms are now displayed as sticks for the '''lysine'''.

|-

|| Click on the '''Actions''' menu on the menu bar.

Select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

|| Click on the '''Actions''' menu again and select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

'''Lysine ''' is now shown as a '''ball and stick '''display.

|-

|| Actions menu again and select the colors option.

Select '''by element''' from the sub menu.

|| Click on the '''Actions''' menu again and select the color option.

Select '''by element''' from the sub menu.

On the panel you can see the '''ball and stick''' model in '''rasmol '''color coding of elements.

Click on '''Select '''option and clear the selection.

|-
|| Type,

select: Amino acid code and position number (example Phe 80)

Press Enter.

Click on the Actions >> Atoms/Bonds >> Show

Actions >> Atoms/Bonds >> ball and stick

|| I will show the steps for one more '''AMINO ACID Phenylalanine 80'''.

At the command line edit the command as shown.

Delete number 33.A

and in its place type 80.A, rest of the command remains as such.

Press '''Enter'''.

|-
|| '''Phenylalanine 80''' is highlighted.
|| '''Phenylalanine 80''' is highlighted.

Go to '''Actions''' menu and click on '''Show''', '''Phenylalanine 80''' is shown in sticks display.

Go to '''Actions''', '''Atoms/Bonds''' and click on '''ball & stick'''.

Go to '''Actions''' again select '''color by element'''.

Click on '''Select''' option and clear the selection.

|-
|| Cursor on the panel.
|| Following the same steps, show all the amino acids in the active-site.

Now receptor-ligand complex with the active site amino acids are shown in '''ball and stick''' display.

|-
|| Click on the '''Select''' menu, choose '''Residue''', from the sub menu choose '''LZ1'''.

Cursor on the panel.

|| To view hydrogen bonds formed by ligand and receptor, select the ligand.

Click on the '''Select''' menu,and choose '''Residue''', from the sub menu choose '''LZ1'''.

On the panel, '''LZ1''' is highlighted in green color.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' FindHBond '''option.

|| Click on the '''Tools '''menu.

Select '''Structure Analysis, '''from the sub-menu choose''' FindHBond '''option.

|-

|| '''H-Bond Parameter''' dialog-box opens.

Click on the check box against '''Label Hydrogen bond with distance'''.

Click on '''Only find H-bonds with at least one end selected.'''

Click on '''Write information to reply log'''.

Click on the '''OK''' button.

|| '''H-Bond Parameters''' dialog-box opens.

In the dialog box,

Fix the color of the '''hydrogen bond''' by clicking the colored box.

I will select yellow color.

Close the Color selection box.

Fix the line width to 3.0 for a thicker line.

* Click on the check box against '''Label Hydrogen bond with distance'''.
* Click on '''Only find H-bonds, with at least one end selected.'''

Uncheck any other check boxes if checked.* And click on '''Write in formation to reply log'''.

Click on '''Apply''' and '''OK''' buttons.

|-

|| Cursor on the panel.
|| Observe the panel.

'''Hydrogen bonds''' are shown as '''pseudo'''-bonds of specified color and line width.

Here we can see only two hydrogen bonds with '''indazole'''.

|-

|| Click on the''' Favorites''' menu on the menu bar.

From the sub menu select '''Reply log''' option.

|| Details of the bonds can be viewed on the '''Reply log'''.

Open '''Reply log '''using '''Favorites''' menu.

Click on '''Favorites''' menu.

From the sub menu select '''Reply log''' option.

A pop-up window opens.

Information about each hydrogen bond is given here.

|-

|| Cursor on the '''Reply log '''pop-up information.

Close the pop-up window.

|| One of the bonds, is formed with '''Leucine''' 83 and '''indazole''' nitrogen.

Another is formed with '''Glutamine''' 81 with hydrogen attached to the nitrogen atom of '''indazole'''.

|-

||Cursor on the panel.
|| On the panel we can see the hydrogen bond distance.

Close the '''Reply log''' window.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' Findclashes/contacts '''option.

|| There is another feature in the''' Tools''' menu under the '''Structure Analysis''' option.

It is '''Findclashes/contacts'''.

A '''dialog box''' opens.

This feature identifies non-polar interactions such as '''Clashes''' and '''Contacts'''.

|-

|| Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

|| Let us identify '''contacts''' of the '''LZ1''' with all other atoms.

Ligand is already selected on the panel.

Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

It shows '''10 atoms designated.'''

Click on the radio button against “'''All other atoms'''”.

|-

|| Click on the radio button against “'''All other atoms'''”.

Point to '''Include intra-molecule contacts.'''

|| In the '''Clash/Contact Parameters''' section, in the '''Default''' click on the '''Contact''' button.

|-

|| Under '''Treatment of Clash/Contact Atoms,''' click on the following check boxes.

* '''Select'''
* '''Draw pseudo-bonds'''
* '''If endpoint atom hidden'''
* '''And Write information to reply log'''

|| Under '''Treatment of Clash/Contact Atoms,'''

click on the following check boxes.

* '''Select ''' and
* '''Draw pseudo-bonds of color'''.

Click on the color box.

In the '''Color Editor '''window I will select green.

Close the color selector.

Check the check box for, '''Write information to reply log'''.

|-
|| Click on the '''OK''' button.

Cursor on the panel.

|| Click on the '''OK''' button.

Observe the panel.

All the contacts of ligand''' LZ1 '''are shown as green lines.

|-
|| Click on the '''Favorites '''menu.

Select '''Reply Log ''' from the sub-menu.

Cursor on the '''Reply Log''' window.

|| Open the '''Reply Log '''using the ''' Favorites ''' menu.

'''Atom-atom contacts''' are listed here.

It shows 21 contacts.

The amino acid residues which made the contact with '''LZ1''' are listed here.

Close the dialog-box.

These residues form the binding site for this receptor-ligand complex.

|-

|| Cursor on the panel.
|| Most of these active site residues are hydrophobic in nature.

Let us create a surface for this complex colored by amino acid '''hydrophobicity'''.

|-

|| Cursor on the panel.
|| Using the '''Presets''' menu let us analyze the hydrophobic surface for this complex.

|-

|| Click on '''Presets''' on the menu bar. From the drop down select '''Interactive 3 hydrophobicity surface'''.

|| Click on '''Presets''' on the menu bar.

From the drop down select '''Interactive 3 hydrophobicity surface'''.

|-

|| Cursor on the panel.
|| The surface represents blue for the most polar residues,

orange for the most hydrophobic,

white for the neutral amino acids.

|-

|| Cursor on the panel.

Rotate and zoom the structure using the mouse.

|| We will rotate and locate the ligand pocket.

As you notice here, most of the ligand binding pocket is '''hydrophobic'''.

|-

|| Click on the''' Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|| The interior of the binding pocket can be viewed using the '''Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|-

|| In the '''Viewing''' window,Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping button'''.

In the pop-up window, check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

Click on '''Close''' button

|| A '''Viewing''' window opens.

You will see a viewing eye and two cutting planes in the '''Viewing''' window.

Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping '''button.

'''Surface Capping''' window opens.

Check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

I will select pink.

Close the color editor.

I will select cap style as solid.

Click on '''Close''' button to close the surface capping window.

|-

|| Change the position of the viewing eye and clipping planes.
|| We can change the position of the viewing eye and clipping planes.

Now we can view the interior of the binding pocket clearly.

You can see clearly that the ligand is attached to the '''hydrophobic pocket'''.

|-
|| '''Slide Number 11'''

'''Conclusion of the Analysis'''
|| Conclusion of the Analysis

The ligand is interacting mostly with the hydrophobic residues inside the binding pocket.

We found many non bonding interactions with the hydrophobic residues.

|-

|| '''Slide Number 12'''

'''Conclusion of the Analysis'''

|| Only a few hydrogen bonds a re expected.

We observed only two hydrogen bonds using the '''Structure Analysis tool.'''

|-
|| Cursor on the panel.
|| More hydrophobic groups on the''' indazole '''will increase the interaction and binding with the active site.

We can generate and analyze more conformers to understand the interactions better.

This brings us to the end of this tutorial.

|-

|| '''Slide Number 13'''

'''Summary'''
|| Let us summarize,

In this tutorial, we have,

Opened the PDB file for the receptor on the '''Chimera''' interface.

Selected and deleted solvent and other residues from the receptor structure.

|-
|| '''Slide Number 14'''

'''Summary'''
|| Added the most preferred conformation of the ligand obtained after autodock runs to the receptor structure.

Showed hydrogen bonds and other interactions of the ligand with the receptor.

|-
|| '''Slide Number 15'''

'''Summary'''
|| Highlighted the active site residues.

Showed the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 16'''

'''Assignment'''
|| As an assignment,

Analyze the dlg files generated for '''1DWD''' receptor-ligand complex using '''UCSF Chimera'''.

https://autodock.scripps.edu/download-autodock4/

|-

|| '''Slide Number 17'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 18'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 19'''

'''Forum'''
|| Please post your timed queries in this forum.
|-
|| '''Slide Number 20'''

'''Acknowledgment '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Visualizing-Docking-using-UCSF-Chimera/English

2024-06-14T12:26:18Z

Snehalathak: Created page with " '''Title of script''': '''Visualizing Docking using UCSF Chimera''' '''Author: '''Dr.Snehalatha Kaliappan and Sruthi Sudhakar '''Keywords: '''Autodock4, docking, UCSF Chi..."

'''Title of script''': '''Visualizing Docking using UCSF Chimera'''

'''Author: '''Dr.Snehalatha Kaliappan and Sruthi Sudhakar

'''Keywords: '''Autodock4, docking, UCSF Chimera, receptor, ligand, residues, hydrogen bonds, video tutorial.

{| border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this spoken tutorial on '''Visualizing Docking using UCSF Chimera.'''

|-
|| '''Slide Number 2'''

'''Learning Objectives'''

|| In this tutorial, we will,

Open the '''PDB '''file for the receptor on the '''Chimera''' interface.

Select and delete solvent and other residues from the receptor structure.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''

|| Add the most preferred docking pose of the ligand to the receptor structure.

Show hydrogen bonds and other interactions.

|-
|| '''Slide Number 4'''

'''Learning Objectives'''
|| Highlight the active site residues.

Show the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 5'''

'''System Requirement'''

|| Here I am using,

'''Ubuntu Linux '''OS version 20.04

AutoDockTools version 1.5.7

UCSF Chimera version 1.17.2

|-
|| '''Slide Number 6'''

'''Pre-requisites'''

'''https://spoken-tutorial.org/tutorial-search/?search_foss=UCSF+Chimera&search_language=English'''

|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on UCSF Chimera interface.

Please refer to the link below for tutorials on UCSF Chimera series.

|-

|| '''Slide number 7'''

'''Code Files'''

||

* The input files required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 8'''

'''Code Files'''

||
* Save the input files in your home directory or working directory

* Make a copy of all the files and then use them for practising.

|-
|| Double-Click on '''Chimera''' icon on the desktop.
|| I will open the '''Chimera''' interface by double-clicking on the shortcut icon on my '''Desktop'''.

'''Chimera''' interface opens.

|-

|| Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

From the '''Open file in the Chimera''' dialog-box, select '''2vta.pdb''' option.

|| Let us load the structure of the receptor on the panel.

Click on the '''File''' menu on the main menu bar.

Select '''Open''' option.

'''Open file in Chimera''' dialog-box opens.

From the dialog-box, select '''2vta.pdb''' option.

Click on the '''Open''' button at the bottom.

|-

|| Cursor on the panel.

Click on the Presets menu.

Select '''Interactive 1 (ribbons)''' option.

|| The receptor-ligand complex loads on the panel.

For me the complex opened in ribbons display.

In your case, it may open in a different format.

You can change it to ribbons format using the '''Presets''' menu on the menu bar.

Select '''Interactive 1 (ribbons)''' option to change the display.

|-
|| Cursor on the panel.

Cursor on the ligand.

CELL DIVISION PROTEIN KINASE 2, amino acids 298, chain A

Ligand is small molecule indazole

|| The receptor here is the '''cyclin dependent kinase inhibitor'''.

The ligand is an '''Indazole''' molecule.

|-
|| Cursor on the ligand.
|| We need to delete indazole, glycerol and water molecules from the structure.

|-

|| Click on the '''Select '''menu, from the drop-down select '''Residues '''option.

Cursor on '''GOL, HOH''' and '''LZ1.'''

|| Click on '''Select '''menu, from the drop-down select '''Residue '''option.

The sub-menu shows 3 residues under the A'''ll nonstandard''' category.

'''GOL, HOH '''and''' LZ1''', that is, '''glycerol''', water and '''Indazole''' respectively.

|-

|| Click on '''GOL'''.
|| Each time I will select a residue, and delete it.

I will click on''' GOL''' which is glycerol.

|-

|| Cursor on glycerol structure.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Cursor on the panel.

|| Glycerol molecules get highlighted on the panel in green color.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''delete''' option.

Glycerol molecules get deleted from the panel.

|-

|| Click on the '''Select '''menu.

From the drop-down select '''Residues '''option choose HOH/LZ1.

Click on the '''Actions''' menu, from the drop-down select '''Atoms/Bonds.'''

From the sub-menu select the '''Delete''' option.

|| Let us delete water molecules and indazole ligand from the structure.

Select water molecules, they are highlighted in green color.

Delete the water molecules from the structure.

Similarly select indazole molecule and delete it.

|-

|| Cursor on the panel.
|| To this receptor structure we will add the best pose conformation of the ligand obtained by '''autodock runs'''.

|-
||Click on the '''File''' menu

select '''Open''', '''Open file in Chimera'''.

dialog-box opens.
|| Click on the '''File''' menu and select '''Open''', '''Open file in Chimera '''dialog-box opens.

Select '''ligand-conf1.pdb''' from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|| From the '''File''' menu, select '''Open''' option.

'''Open file in Chimera '''dialog-box opens.

From the list of files select the '''pdb''' file containing the best pose of the ligand from the '''autodock runs'''.

We had saved this file earlier as '''ligand-conf1.pdb.'''

I will select the file from the list.

In the '''File type''' field select''' PDB''' from the list.

Click on the '''Open''' button at the bottom of the dialog box.

|-
|| Cursor on the panel.
|| On the panel you can see the best conformation of the '''indazole''' added to the receptor structure.

|-

|| '''Slide Number 9'''

'''Chimera Tools for Visualization'''.

|| Using tools in '''Chimera''' we can visualize receptor-ligand interactions.

The two kinds of interactions,

* hydrogen bonds and
* other polar and no n-polar interactions can be visualized.

We can also visualize the active site pocket and surface properties of the receptor.

|-
|| '''Slide Number 10'''

'''Active Site Residues'''

|| From the literature, the following residues form much of the ligand binding pocket:

Lys33, Phe80, Glu81, Phe82, Leu83, His84, Gln85, Asp86, Leu134, and Asp145.

Let us highlight these residues in the structure on the panel.

|-
|| Cursor on the panel.
|| Back to the '''Chimera''' interface.

We will use the command line to select and highlight the active site residues.

|-

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|| Click on the '''Favorites''' menu.

Select the '''Command Line''' option from the drop down.

|-

|| Cursor on the '''Command Line''' at the bottom of the interface.
|| Command line panel opens at the bottom of the interface.

Here you can type the commands in the command field to modify the structure.

|-

|| Type,

select :33.A

Press '''Enter'''.

Cursor on the panel.

Click on the '''Actions''' menu on the menu bar.

|| To select Lysine at position 33 on chain A, I will type , '''select space colon 33 dot A'''

Press '''Enter'''.

On the panel you can see the outline highlighted on the cartoon display.

We will display this amino acid as the ball and stick model.

Click on the '''Actions''' menu on the menu bar.

|-

|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.
|| Select '''Atoms/Bonds, '''choose '''Show '''from the sub-menu.

Atoms are now displayed as sticks for the '''lysine'''.

|-

|| Click on the '''Actions''' menu on the menu bar.

Select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

|| Click on the '''Actions''' menu again and select the '''Atoms/Bonds''' option.

Select '''Ball and stick''' from the menu.

'''Lysine ''' is now shown as a '''ball and stick '''display.

|-

|| Actions menu again and select the colors option.

Select '''by element''' from the sub menu.

|| Click on the '''Actions''' menu again and select the color option.

Select '''by element''' from the sub menu.

On the panel you can see the '''ball and stick''' model in '''rasmol '''color coding of elements.

Click on '''Select '''option and clear the selection.

|-
|| Type,

select: Amino acid code and position number (example Phe 80)

Press Enter.

Click on the Actions >> Atoms/Bonds >> Show

Actions >> Atoms/Bonds >> ball and stick

|| I will show the steps for one more '''AMINO ACID Phenylalanine 80'''.

At the command line edit the command as shown.

Delete number 33.A

and in its place type 80.A, rest of the command remains as such.

Press '''Enter'''.

|-
|| '''Phenylalanine 80''' is highlighted.
|| '''Phenylalanine 80''' is highlighted.

Go to '''Actions''' menu and click on '''Show''', '''Phenylalanine 80''' is shown in sticks display.

Go to '''Actions''', '''Atoms/Bonds''' and click on '''ball & stick'''.

Go to '''Actions''' again select '''color by element'''.

Click on '''Select''' option and clear the selection.

|-
|| Cursor on the panel.
|| Following the same steps, show all the amino acids in the active-site.

Now receptor-ligand complex with the active site amino acids are shown in '''ball and stick''' display.

|-
|| Click on the '''Select''' menu, choose '''Residue''', from the sub menu choose '''LZ1'''.

Cursor on the panel.

|| To view hydrogen bonds formed by ligand and receptor, select the ligand.

Click on the '''Select''' menu,and choose '''Residue''', from the sub menu choose '''LZ1'''.

On the panel, '''LZ1''' is highlighted in green color.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' FindHBond '''option.

|| Click on the '''Tools '''menu.

Select '''Structure Analysis, '''from the sub-menu choose''' FindHBond '''option.

|-

|| '''H-Bond Parameter''' dialog-box opens.

Click on the check box against '''Label Hydrogen bond with distance'''.

Click on '''Only find H-bonds with at least one end selected.'''

Click on '''Write information to reply log'''.

Click on the '''OK''' button.

|| '''H-Bond Parameters''' dialog-box opens.

In the dialog box,

Fix the color of the '''hydrogen bond''' by clicking the colored box.

I will select yellow color.

Close the Color selection box.

Fix the line width to 3.0 for a thicker line.

* Click on the check box against '''Label Hydrogen bond with distance'''.
* Click on '''Only find H-bonds, with at least one end selected.'''

Uncheck any other check boxes if checked.* And click on '''Write in formation to reply log'''.

Click on '''Apply''' and '''OK''' buttons.

|-

|| Cursor on the panel.
|| Observe the panel.

'''Hydrogen bonds''' are shown as '''pseudo'''-bonds of specified color and line width.

Here we can see only two hydrogen bonds with '''indazole'''.

|-

|| Click on the''' Favorites''' menu on the menu bar.

From the sub menu select '''Reply log''' option.

|| Details of the bonds can be viewed on the '''Reply log'''.

Open '''Reply log '''using '''Favorites''' menu.

Click on '''Favorites''' menu.

From the sub menu select '''Reply log''' option.

A pop-up window opens.

Information about each hydrogen bond is given here.

|-

|| Cursor on the '''Reply log '''pop-up information.

Close the pop-up window.

|| One of the bonds, is formed with '''Leucine''' 83 and '''indazole''' nitrogen.

Another is formed with '''Glutamine''' 81 with hydrogen attached to the nitrogen atom of '''indazole'''.

|-

||Cursor on the panel.
|| On the panel we can see the hydrogen bond distance.

Close the '''Reply log''' window.

|-

|| Click on the '''Tools '''menu.

Select '''Structure Analysis''' from the sub-menu choose''' Findclashes/contacts '''option.

|| There is another feature in the''' Tools''' menu under the '''Structure Analysis''' option.

It is '''Findclashes/contacts'''.

A '''dialog box''' opens.

This feature identifies non-polar interactions such as '''Clashes''' and '''Contacts'''.

|-

|| Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

|| Let us identify '''contacts''' of the '''LZ1''' with all other atoms.

Ligand is already selected on the panel.

Click on '''Designate''' in the '''Find Clashes/Contacts dialog box.'''

It shows '''10 atoms designated.'''

Click on the radio button against “'''All other atoms'''”.

|-

|| Click on the radio button against “'''All other atoms'''”.

Point to '''Include intra-molecule contacts.'''

|| In the '''Clash/Contact Parameters''' section, in the '''Default''' click on the '''Contact''' button.

|-

|| Under '''Treatment of Clash/Contact Atoms,''' click on the following check boxes.

* '''Select'''
* '''Draw pseudo-bonds'''
* '''If endpoint atom hidden'''
* '''And Write information to reply log'''

|| Under '''Treatment of Clash/Contact Atoms,'''

click on the following check boxes.

* '''Select ''' and
* '''Draw pseudo-bonds of color'''.

Click on the color box.

In the '''Color Editor '''window I will select green.

Close the color selector.

Check the check box for, '''Write information to reply log'''.

|-
|| Click on the '''OK''' button.

Cursor on the panel.

|| Click on the '''OK''' button.

Observe the panel.

All the contacts of ligand''' LZ1 '''are shown as green lines.

|-
|| Click on the '''Favorites '''menu.

Select '''Reply Log ''' from the sub-menu.

Cursor on the '''Reply Log''' window.

|| Open the '''Reply Log '''using the ''' Favorites ''' menu.

'''Atom-atom contacts''' are listed here.

It shows 21 contacts.

The amino acid residues which made the contact with '''LZ1''' are listed here.

Close the dialog-box.

These residues form the binding site for this receptor-ligand complex.

|-

|| Cursor on the panel.
|| Most of these active site residues are hydrophobic in nature.

Let us create a surface for this complex colored by amino acid '''hydrophobicity'''.

|-

|| Cursor on the panel.
|| Using the '''Presets''' menu let us analyze the hydrophobic surface for this complex.

|-

|| Click on '''Presets''' on the menu bar. From the drop down select '''Interactive 3 hydrophobicity surface'''.

|| Click on '''Presets''' on the menu bar.

From the drop down select '''Interactive 3 hydrophobicity surface'''.

|-

|| Cursor on the panel.
|| The surface represents blue for the most polar residues,

orange for the most hydrophobic,

white for the neutral amino acids.

|-

|| Cursor on the panel.

Rotate and zoom the structure using the mouse.

|| We will rotate and locate the ligand pocket.

As you notice here, most of the ligand binding pocket is '''hydrophobic'''.

|-

|| Click on the''' Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|| The interior of the binding pocket can be viewed using the '''Viewing Controls''' in the '''Tools '''menu.

Select '''Side View''' from the drop down.

|-

|| In the '''Viewing''' window,Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping button'''.

In the pop-up window, check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

Click on '''Close''' button

|| A '''Viewing''' window opens.

You will see a viewing eye and two cutting planes in the '''Viewing''' window.

Check the check box for '''Clip '''at the bottom left.

Click on the '''Surface Capping '''button.

'''Surface Capping''' window opens.

Check the box for '''cap surfaces at clip planes''' and use cap color and cap style.

Click on the color box next to '''use cap color''' to select the color of the cap.

I will select pink.

Close the color editor.

I will select cap style as solid.

Click on '''Close''' button to close the surface capping window.

|-

|| Change the position of the viewing eye and clipping planes.
|| We can change the position of the viewing eye and clipping planes.

Now we can view the interior of the binding pocket clearly.

You can see clearly that the ligand is attached to the '''hydrophobic pocket'''.

|-
|| '''Slide Number 11'''

'''Conclusion of the Analysis'''
|| Conclusion of the Analysis

The ligand is interacting mostly with the hydrophobic residues inside the binding pocket.

We found many non bonding interactions with the hydrophobic residues.

|-

|| '''Slide Number 12'''

'''Conclusion of the Analysis'''

|| Only a few hydrogen bonds a re expected.

We observed only two hydrogen bonds using the '''Structure Analysis tool.'''

|-
|| Cursor on the panel.
|| More hydrophobic groups on the''' indazole '''will increase the interaction and binding with the active site.

We can generate and analyze more conformers to understand the interactions better.

This brings us to the end of this tutorial.

|-

|| '''Slide Number 13'''

'''Summary'''
|| Let us summarize,

In this tutorial, we have,

Opened the PDB file for the receptor on the '''Chimera''' interface.

Selected and deleted solvent and other residues from the receptor structure.

|-
|| '''Slide Number 14'''

'''Summary'''
|| Added the most preferred conformation of the ligand obtained after autodock runs to the receptor structure.

Showed hydrogen bonds and other interactions of the ligand with the receptor.

|-
|| '''Slide Number 15'''

'''Summary'''
|| Highlighted the active site residues.

Showed the receptor-ligand surface and active site pocket.

|-
|| '''Slide Number 16'''

'''Assignment'''
|| As an assignment,

Analyze the dlg files generated for '''1DWD''' receptor-ligand complex using '''UCSF Chimera'''.

https://autodock.scripps.edu/download-autodock4/

|-

|| '''Slide Number 17'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 18'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 19'''

'''Forum'''
|| Please post your timed queries in this forum.
|-
|| '''Slide Number 20'''

'''Acknowledgment '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
||
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Analyzing-Docking-Runs/English

2024-06-07T12:14:13Z

Snehalathak:

'''Title of script''': '''Analyzing Docking Runs'''

'''Author:''' Dr. Snehalatha Kaliappan and Sruthi Sudhakar

'''Keywords''': Autodock4, docking, video tutorial.

{| border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
||Welcome to this spoken tutorial on '''Analyzing Docking Runs.'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''

|| In this tutorial, we will learn to

Open the '''dlg''' file on the '''ADT''' panel

Open and visualize the most favorable conformations of the ligand

Analyze the binding energies of various conformations

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| Analyze clusters of conformations

Open the '''dlg '''file with using a text editor and analyze the data

Export the most favorable docking pose as a '''pdb '''file.
|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using,

'''Ubuntu Linux '''OS version 20.04

AutoDockTools version 1.5.7

gedit version 3.36.2
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on''' AutoDock Tools''' interface
|-
||

'''Slide number 6'''

'''Code Files'''

|| The input files required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 7'''

'''Code Files'''

|| Save the input files in your home directory or working directory

Make a copy of all the files and then use them for practising

|-
|| Open ADT interface using the terminal.
|| I have opened the '''AutoDock Tools '''interface.

Let us analyze the '''dlg''' file generated during the autodock run.

|-
||Click on '''Analyze''' on the menu bar,

from the drop-down choose '''Dockings'''.

Click '''Open '''from the sub menu.
||Click on '''Analyze''' on the menu bar.

From the drop-down choose '''Dockings'''.

Click '''Open '''from the sub menu.
|-
||Cursor on''' Docking Log File''' window.

Select '''2vta.dlg''' from the list of files.

Click on '''Open''' button.
||'''Docking Log File''' window opens.

Select '''2vta.dlg''' from the list of files from your working directory.

Click on the '''Open''' button.

|-
|| Cursor on the pop-up window.

Read the information.

Click '''OK''' to close the pop-up.

||A warning pop-up opens.

Read the message shown on the pop-up.

It gives information about the number of docked conformations.

It is 10 for the present example.

It gives information on how to view the conformations.

Click the '''OK''' button to close the pop-up.
|-
|| Click on '''Analyze, '''from the drop-down choose '''Conformations.'''

'''From '''the sub-menu choose''' Load.'''
|| To visualize the docking results, click on '''Analyze ''' again.

From the drop-down choose '''Conformations'''.

From the sub-menu choose '''Load'''.
|-
|| Cursor on '''2vta Conformation Chooser '''table.
|| '''2vta Conformation Chooser '''window''' '''opens.

In this table, the lower panel has conformations numbered.

You can also see the corresponding docked energy values.
|-
|| Click on 1-1 conformation from the list.

Cursor on the top panel.
|| Click on any conformation number in the list.

The top panel now shows:

Binding energy

kI, inhibition constant

Internal energy

Torsional energy etc.
|-
|| Click “x” on top-right to close the window.
|| Close the window.
|-
|| Click on''' Analyze '''on the menu bar and select '''Macromolecule '''from the dropdown.''' '''

Select '''Open''' from the sub-menu.

Cursor on the receptor.

Zoom-in and show the ligand.
|| Click on''' Analyze '''on the menu bar.

Select '''Macromolecule '''from the dropdown.''' '''

From the sub-menu select '''Open'''.

The receptor is now displayed as lines on the panel.

'''Zoom-in''' to see the receptor-ligand complex.
|-
|| In the left panel, click on oval button on column B for the ligand.
|| Let us visualize the ligand clearly.

We can change the display from lines display to '''sticks '''.

In the left panel, click on the oval button on column '''B''' for the ligand.

The ligand is now displayed in sticks model.

Unselect lines display by clicking on the red oval in column '''L.'''
|-
|| Click on the triangle button in the last column''' CL '''in the ligand row.

Select '''By atom type.'''

Click on '''close''' at the bottom to close the window.
|| Click on the triangle button in the last column '''CL'''.

A menu opens at the bottom of the panel.

By default '''All Representations'''

and ''' balls '''and''' sticks''' check-boxes are checked.

Leave them as such.

We will proceed with the selection.

In the '''Coloring Schemes panel''', I will select '''By atom type.'''

Now we can see the ligand as sticks display and elements in '''Rasmol colors'''.

Click on '''close''' at the bottom to close the window.

|-
|| Cursor on the receptor.

Click on oval button on column R to display receptor as ribbons .

Uncheck the oval button on column L to hide the sticks display.
|| By default the receptor is displayed as lines.

In the left panel, In the '''2vta '''row, click on the oval button in column''' R''' .

Observe the panel, the receptor is now displayed as ribbons.

Uncheck the oval button on column ''' L''' to hide the lines display.

|-
||Click on the triangle button in the last column''' CL '''in the receptor row.

Select '''By rainbow.'''

Click on '''close''' at the bottom to close the window.
||To make the display colorful, click on the triangle button in the last column '''CL'''

A menu opens at the bottom of the left panel.

By default '''All Representations''' and '''Secondarystructure''' check-boxes are checked.

We will proceed with the selection.

From the list of options, select '''By rainbow'''.

The receptor is now seen in rainbow colors.

Users can explore the other options given in the list.

Click on '''close''' at the bottom to close the window.

|-
|| Cursor on the panel.
|| We can also view the conformations of ligand ranked by energy, from lowest to highest.
|-
|| Again click on '''Analyze''' on the menu bar. Select '''Conformations '''from the drop -down.

Select '''play, ranked by energy…'''..

Cursor on the '''ligand '''menu.
|| Click on '''Analyze''', select '''Conformations ''' from the drop-down.

Then select '''play, ranked by energy…'''..

A menu titled '''ligand''' opens with various button options to play.
|-
|| Click on the white arrow play button, on the ligand menu.

Cursor on the panel.

|| Click on the white forward arrow play button on the '''ligand''' menu bar.

On the panel, the 10 conformations are played one after the other in a sequence.
|-
|| Cursor on the “ligand” bar.

Click on the small black arrow buttons to play.
|| Click on the white backward arrow on the '''ligand''' menu to play the conformations in reverse sequence.

This brings the ligand conformation display back to zero.

Conformation number zero represents the initial coordinates of ligand pdbqt that we had used for docking.

Click on the small black forward arrow button to play conformations one-by-one.

I will bring conformation 1 back on the panel by clicking on the black backward button.

|-
|| Click on the 2nd last button (&)on the “ligand” bar.

In the '''Set play options '''dialog, check the check-box for '''Show Info''' at the top.

|| Click on the 2nd last button on the ligand menu bar to change play options.

A pop-up dialog-box '''Set Play options '''opens.

Check the check-box for '''Show Info''' at the top.

|-
|| Cursor on '''Input Conformation '''pop-up box.

Binding energy,ligand efficiency, inhibition constant, and other parameters are listed here

Click on the X top-right to close the pop-up.

|| Another pop-up box called '''Conformation 1 info '''opens.

It gives information of the particular conformation.

Read the information.

Conformation number 1 has the binding energy of -5.66.

The inhibition constant value for this conformation is also given in the information pop-up

Close the '''Conformation 1 Info'''

pop-up box.
|-
|| In the '''Set play options '''dialog,

check the check-box for''' Build H-bonds'''.

Cursor on '''Hydrogen Bonds''' pop-up window.

|| In the '''Set play options '''dialog, check the check-box for ''' Build H-bonds'''.

This will open another pop-up, '''Hydrogen Bonds'''.

This will show the information of hydrogen bonds for the particular conformation.

|-
|| Cursor on '''Hydrogen Bonds''' pop-up window.

Zoom-in the structure on the panel.

|| Only one amino acid ''' Phenylalanine146 ''' is hydrogen bonded to the ligand in this conformation.

Zoom-in the structure on the panel.
|-
|| In the '''Hydrogen Bonds''' pop-up, check the check-box for '''Show Distances'''.

Check-box for''' Show Energy '''and uncheck the checkbox for '''Show Distance'''.
|| In the '''Hydrogen Bonds''' pop-up, check the check-box for '''Show Distances''' if it is not checked.

Here for conformation 1 the distance is 2.237 angstroms.

Now uncheck the checkbox for '''Show Distances'''.

To view the hydrogen bond energies, check the check-box for''' Show Energy.'''

|-
|| Cursor on the panel.
|| On the panel you can see the hydrogen bond energy as -3.069.

|-
|| Click the black arrow button to go to conformation number one.

Cursor on the values.
|| I will click the black arrow button to go to conformation number 2.

In the '''Hydrogen Bonds''' pop-up, check the check-box for '''Show Distances'''.

On the panel we can see hydrogen bond distance as '''2.103''' angstroms.

In the conformation 2 info pop up:

The binding energy is -5.66.

It shows the same binding energy as the previous conformation which was ranked one.

The inhibition constant is 71.01.

Notice that this conformation has a slightly higher inhibition constant when compared to conformation number 1.

Hence it is ranked 2nd.

|-
|| Click on the front black arrow again.

Cursor on the values.
|| Click on the black play button for all the conformations.

You can see the energies and hydrogen bond information of all the conformations.

|-
|| '''Text annotation.'''

(A conformer with -10.5 Kcal better than one with -7kcal)

Cursor on the values.
|| These conformations are ranked from lowest to highest energy.

More negative binding energy with a good pose in the active site would be one of the most favorable poses.

|-
|| Cursor on the values.
|| Bring the most favorable pose, that is conformation 1 back on the panel.

Close all the pop up windows.
|-
|| Cursor on the panel.
|| Let us now view the clustering.
|-
|| Click on '''Analyze''' on the menu bar again and select '''Clusterings''' option.

Cursor on''' Ligand Clusterning''' window.

|| Click on '''Analyze''' on the menu bar again and select '''Clusterings''' option.

Select '''Show '''option from the sub- menu.

'''Ligand Clustering''' window opens.

Here you can see the '''10 conformations '''grouped into 2 clusters.

There are 8 conformations grouped in one cluster and 2 conformations in another cluster.

Table is in the form of a '''2D histogram'''.
|-
|| Open the 2vta.dlg file.

Scroll down to the “CLUSTER ANALYSIS OF CONFORMATIONS” section
|| I will open the ''' 2vta.dlg '''file saved in the home folder using any text editor.

Read the information given here.

Scroll down to the '''CLUSTER ANALYSIS OF CONFORMATIONS ''' section.

The number of conformations is 10.

The 10 conformations are grouped into 2 clusters according to the similarity in their structure.

|-
|| Cursor on '''Clustering Histogram''' table.
|| Clustering Histogram table gives more information.

There are 8 conformations grouped in cluster 1 and 2 conformations in Cluster 2.
|-
|| Cursor on the value.
|| The lowest binding energy -5.66 is for Run 4, which is ranked number 1.

Hence this is the most preferred conformation.
|-
|| Scroll down to the RMSD table.
|| Scroll down to RMSD table.

The '''RMSD''' table gives information about:

ranking, sub-ranking and Binding energy for all the 10 conformations.
|-
|| Cursor on ADT interface.

Click on the black forward arrow to play conformer 1.
|| Back to the ADT interface.

We will save the most favorable pose as a pdb file.

Play the conformation ranked one.

This is the most favorable conformation among the 10 poses.
|-
|| Click on the yellow oval in column S for the ligand.

Select '''Save''' from the drop-down. From the sub-menu, select '''Write PDB'''.

|| Select the ligand by clicking the small oval on the ligand row '''S '''column, that is 1st column on the left panel.

Save this docking pose as a pdb file by clicking on '''File '''menu.

Select '''Save''' from the drop-down.

From the sub-menu, select '''Write PDB'''.

|-
|| Curson on '''Write Options''' dialog box.

Type file name as '''ligand-conf1.pdb'''.

|| '''Write Options''' dialog box opens.

'''Filename''' field is already populated with path and filename.

You can choose to save it at a different location by clicking on the '''Browse''' button.

I will not change the path, but change the file name to '''ligand-conf1.pdb'''.

Click on the '''OK''' button at the bottom of the dialog box.

|-
|| Cursor on the panel.
|| To save another conformation, you can repeat this procedure.

Change the number in the ligand button menu to 2.

Close all the windows.

Select again and Save as''' PDB '''using the File menu.

I will save the file as '''ligand-conf2.pdb'''

|-
|| Show home folder, cursor on ligand-con1.pdb and ligand-con2.pdb files.

Cursor on ligand-con1.pdb file.

|| The pdb files, '''ligand-con1.pdb''' and '''ligand-con2.pdb''' are saved in the home folder.

These files can be read by '''Pymol''',''' Chimera''' or '''Jmol''' for further analysis and for the generation of high-resolution images.

|-
|| Only Narration
|| This brings us to the end of this tutorial.

Let us summarize,

|-
|| '''Slide Number 8'''

'''Summary'''
|| In this tutorial, we,

Opened the dlg file on the ADT panel.

Opened and visualize the most favorable conformations of ligand.

Analyzed the binding energies of various conformations.

|-
|| '''Slide Number 9'''

'''Summary'''
|| Analyzed clusters of conformations.

Opened the dlg file using a text editor and analyzed the data.

Exported the most favorable docking pose as a pdb file.
|-
|| '''Slide Number 10'''

'''Assignment'''
|| As an assignment,

Analyze the dlg files generated for 1DWD receptor-ligand complex.

https://autodock.scripps.edu/download-autodock4/

|-
|| '''Slide''' '''Number 11'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.
|-
|| '''Slide Number 12'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.
|-
|| '''Slide Number 13'''

'''Forum'''
||
* Please post your timed queries in this forum.

|-
|| '''Slide''' '''Number 14'''

'''Acknowledgement '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
|| '''Slide''' '''Number 14'''

'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}

AutoDock4/C2/Analyzing-Docking-Runs/English

2024-05-31T11:10:12Z

Snehalathak: Created page with " '''Title of script''': '''Analyzing Docking Runs''' '''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar''' '''Keywords: Autodock4, docking, video tutorial.''' {|..."

'''Title of script''': '''Analyzing Docking Runs'''

'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''

'''Keywords: Autodock4, docking, video tutorial.'''

{| border=1
|-
|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
||Welcome to this spoken tutorial on '''Analyzing Docking Runs.'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''

|| In this tutorial, we will learn to

Open the '''dlg''' file on the '''ADT''' panel

Open and visualize the most favorable conformations of the ligand

Analyze the binding energies of various conformations

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| Analyze clusters of conformations

Open the '''dlg '''file with using a text editor and analyze the data

Export the most favorable docking pose as a '''pdb '''file.
|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using,

'''Ubuntu Linux '''OS version 20.04

AutoDockTools version 1.5.7

gedit version 3.36.2
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on''' AutoDock Tools''' interface
|-
||

'''Slide number 6'''

'''Code Files'''

|| The inputfiles required for this tutorial are available in the '''Code files''' link.
* Please download and extract the files.

|-
|| '''Slide number 7'''

'''Code Files'''

|| Save the input files in your home directory or working directory

Make a copy of all the files and then use them for practising

|-
|| Open ADT interface using the terminal.
|| I have opened the '''AutoDock Tools '''interface.

Let us analyze the dlg file generated during the autodock run.

|-
||Click on '''Analyze''' on the menu bar,

from the drop-down choose '''Dockings'''.

Click '''Open '''from the sub menu.
||Click on '''Analyze''' on the menu bar.

From the drop-down choose '''Dockings'''.

Click '''Open '''from the sub menu.
|-
||Cursor on''' Docking Log File''' window.

Select '''2vta.dlg''' from the list of files.

Click on '''Open''' button.
||'''Docking Log File''' window opens.

Select '''2vta.dlg''' from the list of files from your working directory.

Click on the '''Open''' button.

|-
|| Cursor on the pop-up window.

Read the information.

Click '''OK''' to close the pop-up.

||A warning pop-up opens. Read the message shown on the pop-up.

It gives information about the number of docked conformations.

It is 10 for the present example.

It gives information on how to view the conformations.

Click the '''OK''' button to close the pop-up.
|-
|| Click on '''Analyze, '''from the drop-down choose '''Conformations.'''

'''From '''the sub-menu choose''' Load.'''
|| To visualize the docking results, click on '''Analyze '''again.

From the drop-down choose '''Conformations'''.

From the sub-menu choose '''Load.'''
|-
|| Cursor on '''2vta Conformation Chooser '''table.
|| '''2vta Conformation Chooser '''window''' '''opens.

In this table, the lower panel has conformations numbered.

You can also see the corresponding docked energy values.
|-
|| Click on 1-1 conformation from the list.

Cursor on the top panel.
|| Click on any conformation number in the list.

The top panel now shows:

Binding energy

kI, inhibition constant

Internal energy

Torsional energy etc.
|-
|| Click “x” on top-right to close the window.
|| Close the window.
|-
|| Click on''' Analyze '''on the menu bar and select '''Macromolecule f'''rom the dropdown.''' '''

Select '''Open''' from the sub-menu.

Cursor on the receptor.

Zoom-in and show the ligand.
|| Click on''' Analyze '''on the menu bar.

Select '''Macromolecule f'''rom the dropdown.''' '''

From the sub-menu select '''Open'''.

The receptor is now displayed as lines on the panel.

'''Zoom-in''' to see the receptor-ligand complex.
|-
|| In the left panel, click on oval button on column B for the ligand.
|| Let us visualize the ligand clearly.

We can change the display from lines display to '''sticks '''display.

In the left panel, click on the oval button on column '''B''' for the ligand.

The ligand is now displayed in sticks model.

Unselect lines display by clicking on the red oval in column '''L.'''
|-
|| Click on the triangle button in the last column''' CL '''in the ligand row.

Select '''By atom type.'''

Click on '''close''' at the bottom to close the window.
|| Click on the triangle button in the last column '''CL.'''

A menu opens at the bottom of the panel.

By default '''All Representations'''

and ''' balls '''and''' sticks''' check-boxes are checked.

Leave them as such.

We will proceed with the selection.

In the coloring '''Scheme panel''', I will select '''By atom type.'''

Now we can see the ligand as sticks display and elements in '''Rasmol colors.'''

Click on '''close''' at the bottom to close the window.

|-
|| Cursor on the receptor.

Click on oval button on column R to display receptor as ribbons .

Uncheck the oval button on column L to hide the sticks display.
|| By default the receptor is displayed as lines.

In the left panel, In the '''2vta '''row, click on the oval button in column''' R.'''

Observe the panel, the receptor is now displayed as ribbons.

Uncheck the oval button on column''' L''' to hide the lines display.

|-
||Click on the triangle button in the last column''' CL '''in the receptor row.

Select '''By rainbow.'''

Click on '''close''' at the bottom to close the window.
||To make the display colorful, click on the triangle button in the last column '''CL'''

A menu opens at the bottom of the left panel.

By default '''All Representations''' and '''Secondarystructure''' check-boxes are checked.

We will proceed with the selection.

From the list of options, select '''By rainbow.'''

The receptor is now seen in rainbow colors.

Users can explore the other options given in the list.

Click on '''close''' at the bottom to close the window.

|-
|| Cursor on the panel.
|| We can also view the conformations of ligand ranked by energy, from lowest to highest.
|-
|| Again click on '''Analyze''' on the menu bar. Select '''Conformations '''from the drop -down.

Select '''play, ranked by energy…'''..

Cursor on the '''ligand '''menu.
|| Click on '''Analyze''', select '''Conformations '''from the drop-down.

Then select '''play, ranked by energy…'''..

A menu titled '''ligand''' opens with various button options to play.
|-
|| Click on the white arrow play button, on the ligand menu.

Cursor on the panel.

|| Click on the white forward arrow play button on the '''ligand''' menu bar.

On the panel, the 10 conformations are played one after the other in a sequence.
|-
|| Cursor on the “ligand” bar.

Click on the small black arrow buttons to play.
|| Click on the white backward arrow on the '''ligand''' menu to play the conformations in reverse sequence.

This brings the ligand conformation display back to zero.

Conformation number zero represents the initial coordinates of ligand pdbqt that we had used for docking.

Click on the small black forward arrow button to play conformations one-by-one.

I will bring conformation 1 back on the panel by clicking on the black backward button.

|-
|| Click on the 2nd last button (&)on the “ligand” bar.

In the '''Set play options '''dialog, check the check-box for '''Show Info''' at the top.

|| Click on the 2nd last button on the ligand menu bar to change play options.

A pop-up dialog-box '''Set play options '''opens.

Check the check-box for '''Show Info''' at the top.

|-
|| Cursor on '''Input Conformation '''pop-up box.

Binding energy,ligand efficiency, inhibition constant, and other parameters are listed here

Click on the X top-right to close the pop-up.

|| Another pop-up box called '''Conformation 1 info '''opens.

It gives information of the particular conformation.

Read the information.

Conformation number 1 has the binding energy of -5.66.

The inhibition constant value for this conformation is also given in the information pop-up

Close the '''Conformation 1 Info'''

pop-up box.
|-
|| In the '''Set play options '''dialog,

check the check-box for''' Build H-bonds'''.

Cursor on '''Hydrogen Bonds''' pop-up window.

|| In the '''Set play options '''dialog, check the check-box for''' Build H-bonds'''.

This will open another pop-up, '''Hydrogen Bonds'''.

This will show the information of hydrogen bonds for the particular conformation.

|-
|| Cursor on '''Hydrogen Bonds''' pop-up window.

Zoom-in the structure on the panel.

|| Only one amino acid''' Phenylalanine146 '''is hydrogen bonded to the ligand in this conformation.

Zoom-in the structure on the panel.
|-
|| In the '''Hydrogen Bonds''' pop-up, check the check-box for '''Show Distances'''.

Check-box for''' Show Energy '''and uncheck the checkbox for '''Show Distance'''.
|| In the '''Hydrogen Bonds''' pop-up, check the check-box for '''Show Distances''' if it is not checked.

Here for conformation 1 the distance is 2.237 angstroms.

Now uncheck the checkbox for '''Show Distance'''.

To view the hydrogen bond energies, check the check-box for''' Show Energy.'''

|-
|| Cursor on the panel.
|| On the panel you can see the hydrogen bond energy as -3.069.

|-
|| Click the black arrow button to go to conformation number one.

Cursor on the values.
|| I will click the black arrow button to go to conformation number 2.

In the '''Hydrogen Bonds''' pop-up, check the check-box for '''Show Distances'''.

On the panel we can see hydrogen bond distance as '''2.103''' angstroms.

In the conformation 2 info pop up:

The binding energy is -5.66.

It shows the same binding energy as the previous conformation which was ranked one.

The inhibition constant is 71.01.

Notice that this conformation has a slightly higher inhibition constant when compared to conformation number 1.

Hence it is ranked 2nd.

|-
|| Click on the front black arrow again.

Cursor on the values.
|| Click on the black play button for all the conformations.

You can see the energies and hydrogen bond information of all the conformations.

|-
|| '''Text annotation.'''

(A conformer with -10.5 Kcal better than one with -7kcal)

Cursor on the values.
|| These conformations are ranked lowest to highest energy.

More negative binding energy with a good pose in the active site would be one of the most favorable poses.

|-
|| Cursor on the values.
|| Bring the most favorable pose, that is conformation 1 back on the panel.

Close all the pop up windows.
|-
|| Cursor on the panel.
|| Let us now view the clustering.
|-
|| Click on '''Analyze''' on the menu bar again and select '''Clusterings''' option.

Cursor on''' Ligand Clusterning''' window.

|| Click on '''Analyze''' on the menu bar again and select '''Clusterings''' option.

Select '''Show '''option from the sub- menu.

'''Ligand Clustering''' window opens.

Here you can see the '''10 conformations '''grouped into 2 clusters.

There are 8 conformations grouped in one cluster and 2 conformations in another cluster.

Table is in the form of a '''2D histogram'''.
|-
|| Open the 2vta.dlg file.

Scroll down to the “CLUSTER ANALYSIS OF CONFORMATIONS” section
|| I will open the''' 2vta.dlg '''file saved in the home folder using any text editor.

Read the information given here.

Scroll down to the '''CLUSTER ANALYSIS OF CONFORMATIONS '''section.

The number of conformations is 10.

The 10 conformations are grouped into 2 clusters according to the similarity in their structure.

|-
|| Cursor on '''Clustering Histogram''' table.
|| Clustering Histogram table gives more information.

There are 8 conformations grouped in cluster 1 and 2 conformations in Cluster 2.
|-
|| Cursor on the value.
|| The lowest binding energy -5.66 is for Run 4, which is ranked number 1.

Hence this is the most preferred conformation.
|-
|| Scroll down to the RMSD table.
|| Scroll down to RMSD table.

The '''RMSD''' table gives information about:

ranking, sub-ranking and Binding energy information for all the 10 conformations.
|-
|| Cursor on ADT interface.

Click on the black forward arrow to play conformer 1.
|| Back to the ADT interface.

We will save the most favorable pose as a pdb file.

Play the conformation ranked one.

This is the most favorable conformation among the 10 poses.
|-
|| Click on the yellow oval in column S for the ligand.

Select '''Save''' from the drop-down. From the sub-menu, select '''Write PDB'''.

|| Select the ligand by clicking the small oval on the ligand row '''S '''column, that is 1st column on the left panel.

Save this docking pose as a pdb file by clicking on '''File '''menu.

Select '''Save''' from the drop-down. From the sub-menu, select '''Write PDB'''.

|-
|| Curson on '''Write Options''' dialog box.

Type file name as '''ligand-conf1.pdb'''.

|| '''Write Options''' dialog box opens.

'''Filename''' field is already populated with path and filename.

You can choose to save it at a different location by clicking on the '''Browse''' button.

I will not change the path, but change the file name to '''ligand-conf1.pdb'''.

Click on the '''OK''' button at the bottom of the dialog box.

|-
|| Cursor on the panel.
|| To save another conformation, you can repeat this procedure.

Change the number in the ligand button menu to 2.

Close all the windows.

Select again and Save as''' PDB '''using the File menu.

I will save the file as '''ligand-conf2.pdb'''

|-
|| Show home folder, cursor on ligand-con1.pdb and ligand-con2.pdb files.

Cursor on ligand-con1.pdb file.

|| The pdb files, '''ligand-con1.pdb''' and '''ligand-con2.pdb''' are saved in the home folder.

These files can be read by '''Pymol''',''' Chimera''' or '''Jmol''' for further analysis and for the generation of high-resolution images.

|-
|| Only Narration
|| This brings us to the end of this tutorial.

Let's summarize,

|-
|| '''Slide Number 8'''

'''Summary'''
|| In this tutorial, we,

Opened the dlg file on the ADT panel.

Opened and visualize the most favorable conformations of ligand.

Analyzed the binding energies of various conformations.

|-
|| '''Slide Number 9'''

'''Summary'''
|| Analyzed clusters of conformations.

Opened the dlg file using a text editor and analyzed the data.

Exported the most favorable docking pose as pdb file.
|-
|| '''Slide Number 10'''

'''Assignment'''
|| As an assignment,

Analyze the dlg files generated for 1DWD receptor-ligand complex.

https://autodock.scripps.edu/download-autodock4/

|-
|| '''Slide''' '''Number 11'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.
|-
|| '''Slide''' '''Number 12'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.
|-
|| '''Slide''' '''Number 13'''

'''Forum'''
||
* Please post your timed queries in this forum.

|-
|| '''Slide''' '''Number 14'''

'''Acknowledgement '''
|| Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
|| '''Slide''' '''Number 15'''

'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}

Inkscape-Techniques-to-Create-Vector-Graphics/C2/3D-Drawing-of-a-Pair-of-Headphones/English

2024-05-31T08:58:45Z

Snehalathak:

'''Title of script: 3D Drawing of a Pair of Headphones'''

'''Author''': Shital

'''Keywords''': Inkscape, headphones, Gradient, Difference, Union, Bezier tool,3D Drawing of a pair of Headphones, Video tutorial.

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide-1'''

'''Opening Slide'''
|| Welcome to this Spoken Tutorial on '''3D Drawing of a Pair of Headphones''' using '''Inkscape'''.
|-
|| '''Slide'''

'''Learning Objectives'''
|| In this tutorial we will,

* Import a headphone’s picture into '''Inkscape'''
* Use '''Circle tool''', '''Difference '''and '''Union''' options to create speaker’s cups and cushions
* Use '''Bezier tool''' to create a headband
* Create shadows and light using '''Gradient tool''' to bring depth to the drawing
* Create a 3D realistic drawing of a pair of Headphones

|-
|| '''Slide'''

'''System Requirement'''
|| To record this tutorial, I am using,
* '''Mac''' OS version 10.14.6
* '''Inkscape '''version 1.2.2

|-
|| '''Slide'''

'''Prerequisites'''

http://spoken-tutorial.org
|| To understand this tutorial, learner requires a good command of Inkscape tools.

For the prerequisite tutorials on '''Inkscape '''please visit this website.

|-
|| '''Slide'''

'''Code Files'''
|| The image used in this tutorial is given in the '''Code Files''' link.

Please download and extract the file.

Make a copy and then use it while practising.
|-
|| Open '''Inkscape'''
|| Let us open '''Inkscape.'''
|-
|| '''File '''>> '''Document Properties >>

Orientation ''' >> Select the ''''Landscape '''Orientation'''

Click on '''Close button(X)'''
|| Go to '''File ''' and click on '''Document Properties'''.

In the dialog box, select ''' Landscape Orientation'''.

Close the '''Document Properties '''dialog box.
|-
|| Go to '''File'''>> Click on '''Save'''.

In the Save dialog box type the filename as '''3D Drawing of a pair of Headphones.svg'''.

Click on '''Save''' button.
|| Let us now save the file.

Go to File. Click on '''Save'''.

In the '''Save''' dialog box type the filename as '''3D- Drawing-of-a-pair-of-Headphones.svg'''.

Click on '''Save''' button.

Please remember to save the file often while drawing.
|-
|| '''File '''>> '''Import >>

Select file to import '''>>

'''Desktop ''' >> Select the file >>

Click on '''Open '''.
|| Go to '''File '''and click on '''Import.'''

In the dialog box''' Select file to import'''.

Go to the location on your computer where the image is saved.

Select '''File''' and click on '''Open'''.
|-
|| '''Jpeg image bitmap import '''window opens.

Click on''' Ok''' >>

Close the dialog box >>

Point out imported image.

|| '''Jpeg bitmap image import '''window opens.

Click the '''OK ''' button to close the window.

Now, the image is loaded on the canvas.

Scale and adjust the reference image.
|-
|| Go to the '''Layers panel''' located on the right side of the interface.

>> Double click on the selected Layer >>

Rename the name as ‘Reference’

|| Go to the '''Layers panel''' located at the right side of the interface.

Double click on the selected Layer and rename the layer as ‘'''Reference'''’.

|-
|| Point out imported image >> '''Menu bar'''

>> Click on '''Object''' >>

Click on '''Fill and Stroke '''

||This image is for reference so you can decrease its '''Opacity'''.

To decrease the opacity, go to the''' Object''' menu on the '''Menu bar.'''

Click on ''' Fill and Stroke'''.
|-
|| '''Fill tab '''>> Change '''Opacity.'''
|| '''Fill and stroke '''window opens on the right side of the Interface.

Let us now adjust the '''Opacity'''.

Drag the opacity slider located at the bottom of the '''Fill and Stroke''' window.

|-
|| '''Layers panel''' >>

Click on lock icon.

|| The reference image must be retained as a reference as long as you work.

Go to the '''Layers''' panel.

Click the lock icon to lock the reference image layer.
|-
|| '''Slide'''

'''Add a Separate Layer'''
|| Please remember to add a separate layer for each part of the drawing.

Rename the layer with a proper name.

For example. '''Speaker’s cushion-Left''', '''Speaker’s cushion-Right''', '''Headband''' and others.

|-
|| '''Toolbar''' >> Select the '''Circle tool'''

>>'''Canvas'''>> Draw a circle

>> '''Fill''' >> '''Opacity''' Change the value to 100.

|| From the '''Toolbox''', Select the '''Circle tool'''.

On the layer of the Speaker’s cushions left,

Draw a circle.

Ensure that the Opacity value is set to 100

|-
|| '''Canvas''' Draw a circle

>>'''Fill>> '''Remove the fill'''

>>''' Scale >> Rotate
|| Go to '''Fill''' tab and remove the '''Fill'''.

Make sure that the '''Stroke''' option is selected in the '''Fill and stroke ''' tab.

Scale and rotate the circle as required.

|-
|| '''Canvas'''>> '''Edit'''

>> '''Duplicate>'''>>

select one of the duplicated circles

>> Scale and adjust >>

Select remaining one of the duplicated circles drag and adjust
|| To make the inside part of the speaker's cushion, adjust the circle as shown.

Go to '''Edit menu '''and click on '''Duplicate ''' to make a copy of the drawn circle.

Duplicate the drawn circle twice.

The duplicated circles are positioned in the same location as the drawn circle.

Select one of the duplicated circles.

Drag and adjust it as shown.

|-
|| '''Canvas >> Path >>

'''Click on '''Difference'''
|| Now, select the shifted circle and the remaining duplicated circle.

Go to the '''Path''' and click on '''Difference.'''

|-
|| '''Canvas''' >>
Duplicate the remaining one of the duplicated circle
>> Scale and adjust
|| The duplicated circles were used to create the inside part of the speaker's cushion.

Only the initial circle remains on the canvas.

To create the front part of the speaker's cushion.

Create a duplicate of the initial circle that is still on the canvas.

Scale and adjust as shown.

|-
|| '''Canvas''' >>

Duplicate the adjusted circle twice

>> Move and adjust one of the duplicated circles

>> Select the adjusted circle and the remaining duplicated circle.

|| Now, let us create the middle part of the speaker's cushion.

Duplicate the adjusted circle twice.

Move and adjust one of the duplicated circles as demonstrated.

Select the adjusted circle and the remaining duplicated circle.
|-
|| '''Path'''>> Click on '''Union'''
|| Go to '''Path''' and click on '''Union'''.

|-
|| '''Canvas'''>> ''' Editing nodes'''.
|| Adjust circles by editing the nodes as demonstrated.

|-
|| '''Canvas'''>> Duplicate the edited shape twice

>> Select one of the duplicated shape

>> Move and adjust as demonstrated.
|| To make the cushion's backside, duplicate the edited shape twice.

Select one of the duplicated shapes.

Move and adjust as demonstrated.
|-
||
|| To get the difference,

Please note:

The shape from which we want to get the difference has to be kept behind the current shape.

|-
|| '''Canvas ''' >>

Select edited shape and one of the duplicated shape

>>''' Path''' >> Click on''' Difference'''

|| Select the edited shape and the remaining duplicated shape.

Go to '''Path''' and click on''' Difference'''.

|-
|| '''Canvas''' >>

Duplicate the shape resulting from the difference.

'''>> Layers panel '''Create a new''' Layer '''named

'''Speaker cup Left >>

'''Select the '''Layer '''of the duplicated shape from the''' Layers panel'''

>>Drag and drop into the '''Layer''' of the''' Speaker cup Left'''

>>''' Canvas>>'''

adjust as shown >>
Duplicate the adjusted shape and edit it for the remaining part of the speaker’s cup.

|| To make the speaker’s cup, duplicate the shape resulting from the difference.

Create a new''' Layer '''named '''Speaker cup Left'''.

Select the '''Layer '''of the duplicated shape from the''' Layers panel'''.

Drag and drop into the '''Layer''' of the''' Speaker cup Left'''

Go to the '''Canvas''' and adjust as shown.

Duplicate the adjusted shape and edit it for the remaining part of the speaker’s cup.

|-
|| Cursor on the '''Canvas'''.
|| Now, add new layers to the right side speaker’s cushion and speaker’s cup.

Create the speaker’s cushion and speaker’s cup on the right side as before.
|-
|| '''Toolbar''' >> '''Bezier tool>>

Canvas'''>>Draw headband
||
Go to '''Toolbox'''. Select the '''Bezier tool'''.

Using the '''Bezier''' tool let us draw the various parts of the headband.

Users can draw the headband using the bezier tool as seen here.

The headband parts will look as shown.
|-
|| '''Layer panel >>

'''Select reference image >>

'''Canvas'''>>Move, scale and adjust >>

'''Fill and Stroke '''>>''' Opacity'''
|| After all the parts are drawn, select the reference image '''Layer'''.

Click on the lock icon to unlock the '''Layer'''.

Go to '''Canvas.'''

Move, scale and adjust the reference image.

Make sure to increase the opacity to 100 before adding colors.

|-
|| '''Canvas''' >>

Select shape one by one >>

Fill colors>>''' Layers panel'''

>> Arrange layers

|| Select the shapes of the speaker’s cushions, speaker’s cups, and headband one by one.

Fill the color by''' '''picking a suitable color from the reference image as shown'''.'''

Go to the '''Layers panel'''.

Arrange layers from the '''Layers panel''' while filling colors as demonstrated.

|-
|| '''Canvas''' >>

Select all parts of the drawing >>

'''Stroke paint''' >>Click on '''No paint

>> Canvas >> '''point towards the gap
|| Select all parts of the drawing

Go to the '''Stroke paint''' tab.

Click on '''No paint ''' to remove the outlines from drawing.

Check the gaps between the shapes and adjust them.
|-
|| '''Canvas''' >>

Fill the '''Linear Gradient''' using '''Gradient tool'''.
|| Select the shapes of the speaker’s cushion, speaker’s cup, and headband one by one.

And apply the gradient.

To do so, Select the '''Gradient tool''' option from the '''Toolbar'''.

And Choose the '''Create linear gradient '''option from the '''Tool controls bar.'''

Apply the gradient by choosing a suitable color from the reference image

Adjust the gradient as demonstrated.

You can use '''Linear gradient ''' or ''' Radial gradient ''' as per the requirement.

This method helps to create depth and gives 3D realistic drawing.
|-
|| '''Canvas'''
|| For more details, create shadows and highlights using the '''Bezier tool'''.

|-
|| '''FIll >> '''Increase '''Blur '''value

>> '''Layers panel >>

'''Hide reference layer by clicking on eye icon
|| Now, go to the '''Fill tab.'''

Increase the '''Blur '''value for merging two colors as needed.

Add more details as applicable.

To hide the reference image, go to the ''' Layers panel'''.

Click on the eye icon of the reference image '''Layer'''.
|-
|| '''Layers panel >>

'''Select all the layers '''

>> Object Menu >>

Group>>Layers panel

>> '''Double click on the''' Group layer '''

and rename it as''' Headphone'''
|| Select all the parts from the '''Layers panel '''at once.

Go to '''Object''' and click on '''Group.'''

Double click on the '''Group layer''' from the ''' Layers panel''' and rename it as '''Headphone.'''
|-
|| '''Filter >> Shadows and Glows

>>Drop Shadow>> Options >>

'''Adjust the parameters >>

'''Shadow type'''>>'''Outer

>>Preview>> '''click on the checkbox'''

>>''' '''Apply'''
|| Go to '''Filters menu'''.

Navigate to '''Shadows and Glows ''' and click on the '''Drop Shadow''' from the submenu.

'''Drop Shadow''' window opens'''.

Click on the '''Options '''and adjust the parameters as shown.

Make sure the '''Outer''' option is selected from the drop down menu of '''Shadow type'''.

To view the preview, click on the checkbox labeled "'''Live''' '''Preview'''".

Click on '''Apply'''. Close the window.
|-
|| '''Toolbar >> '''Select

'''Rectangle tool>>

Canvas>>'''Draw rectangle on the''' Canvas>> Layers panel>>

'''Rename the layer and arrange>>Select color from the
'''Palette'''

|| Select''' Rectangle tool '''from the '''Toolbox.'''

Draw a rectangle on the '''Canvas '''as demonstrated.

Rename the''' Layer''' as''' Background '''from the '''Layers panel'''.

Arrange the '''Layer '''behind the''' Layer''' of the head Phone.

Pick color from '''Palette '''as shown.

Now the 3D Drawing of a pair of headphones''' '''is ready.
|-
|| Point to the headphone
|| Similarly, you can create various other objects using this method.
|-
||'''Slide'''

'''Summary'''
|| This brings us to the end of this tutorial.

Let us summarize.

In this tutorial we have learnt to-

* Import a headphone’s picture into '''Inkscape'''
* Use '''Circle tool''', '''Difference '''and '''Union''' options to create speaker’s cups and cushions
* Use '''Bezier tool''' to create headband
* Create shadows and light using '''Gradient tool''' to bring depth to the drawing
* Create a 3D realistic drawing of a pair of headphones

|-
|| '''Slide'''

'''Assignment'''
|| Here is an assignment for you.
* Create the drawing of an ironbox from the image given in the Code files

|-
|| Completed assignment
|| Your completed assignment should look like this.
|-
||'''Slide'''

'''About Spoken Tutorial'''

|| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|'''Slide'''

'''Workshop'''

|| We conduct workshops using spoken tutorials and give certificates.

For more details, please write to us.
|-
||'''Slide'''

'''Spoken Tutorial Forum slide'''
||Do you have questions in THIS Spoken Tutorial?

Please visit this site

Choose the minute and second where you have the question

Explain your question briefly

The Spoken Tutorial project will ensure an answer

You will have to register to ask questions
|-
||'''Slide'''

'''Acknowledgment'''
|| Spoken Tutorial project was established by the Ministry of Education Government of India.
|-
||
|| This tutorial is contributed by Shital Joshi from IIT Bombay.

Thank you for joining.
|-
|}

Inkscape-Techniques-to-Create-Vector-Graphics/C2/3D-Drawing-of-a-Pair-of-Headphones/English

2024-05-31T07:08:08Z

Snehalathak:

'''Title of script: 3D Drawing of a Pair of Headphones'''

'''Author''': Shital

'''Keywords''': Inkscape, headphones, Gradient, Difference, Union, Bezier tool,3D Drawing of a pair of Headphones, Video tutorial.

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide'''

'''Opening Slide'''
|| Welcome to this Spoken Tutorial on '''3D Drawing of a Pair of Headphones''' using '''Inkscape'''.
|-
|| '''Slide'''

'''Learning Objectives'''
|| In this tutorial we will,

* Import a headphone’s picture into '''Inkscape'''
* Use '''Circle tool''', '''Difference '''and '''Union''' options to create speaker’s cups and cushions
* Use '''Bezier tool''' to create a headband
* Create shadows and light using '''Gradient tool''' to bring depth to the drawing
* Create a 3D realistic drawing of a pair of Headphones

|-
|| '''Slide'''

'''System Requirement'''
|| To record this tutorial, I am using,
* '''Mac''' OS version 10.14.6
* '''Inkscape '''version 1.2.2

|-
|| '''Slide'''

'''Prerequisites'''

http://spoken-tutorial.org
|| To understand this tutorial, learner requires a good command of Inkscape tools.

For the prerequisite tutorials on '''Inkscape '''please visit this website.

|-
|| '''Slide'''

'''Code Files'''
|| The image used in this tutorial is given in the '''Code Files''' link.

Please download and extract the file.

Make a copy and then use it while practising.
|-
|| Open '''Inkscape'''
|| Let us open '''Inkscape.'''
|-
|| '''File '''>> '''Document Properties >>

Orientation ''' >> Select the ''''Landscape '''Orientation'''

Click on '''Close button(X)'''
|| Go to '''File ''' and click on '''Document Properties'''.

In the dialog box, select ''' Landscape Orientation'''.

Close the '''Document Properties '''dialog box.
|-
|| Go to '''File'''>> Click on '''Save'''.

In the Save dialog box type the filename as '''3D Drawing of a pair of Headphones.svg'''.

Click on '''Save''' button.
|| Let us now save the file.

Go to File. Click on '''Save'''.

In the '''Save''' dialog box type the filename as '''3D- Drawing-of-a-pair-of-Headphones.svg'''.

Click on '''Save''' button.

Please remember to save the file often while drawing.
|-
|| '''File '''>> '''Import >>

Select file to import '''>>

'''Desktop ''' >> Select the file >>

Click on '''Open '''.
|| Go to '''File '''and click on '''Import.'''

In the dialog box''' Select file to import'''.

Go to the location on your computer where the image is saved.

Select '''File''' and click on '''Open'''.
|-
|| '''Jpeg image bitmap import '''window opens.

Click on''' Ok''' >>

Close the dialog box >>

Point out imported image.

|| '''Jpeg bitmap image import '''window opens.

Click the '''OK ''' button to close the window.

Now, the image is loaded on the canvas.

Scale and adjust the reference image.
|-
|| Go to the '''Layers panel''' located on the right side of the interface.

>> Double click on the selected Layer >>

Rename the name as ‘Reference’

|| Go to the '''Layers panel''' located at the right side of the interface.

Double click on the selected Layer and rename the layer as ‘'''Reference'''’.

|-
|| Point out imported image >> '''Menu bar'''

>> Click on '''Object''' >>

Click on '''Fill and Stroke '''

||This image is for reference so you can decrease its '''Opacity'''.

To decrease the opacity, go to the''' Object''' menu on the '''Menu bar.'''

Click on ''' Fill and Stroke'''.
|-
|| '''Fill tab '''>> Change '''Opacity.'''
|| '''Fill and stroke '''window opens on the right side of the Interface.

Let us now adjust the '''Opacity'''.

Drag the opacity slider located at the bottom of the '''Fill and Stroke''' window.

|-
|| '''Layers panel''' >>

Click on lock icon.

|| The reference image must be retained as a reference as long as you work.

Go to the '''Layers''' panel.

Click the lock icon to lock the reference image layer.
|-
|| '''Slide'''

'''Add a Separate Layer'''
|| Please remember to add a separate layer for each part of the drawing.

Rename the layer with a proper name.

For example. '''Speaker’s cushion-Left''', '''Speaker’s cushion-Right''', '''Headband''' and others.

|-
|| '''Toolbar''' >> Select the '''Circle tool'''

>>'''Canvas'''>> Draw a circle

>> '''Fill''' >> '''Opacity''' Change the value to 100.

|| From the '''Toolbox''', Select the '''Circle tool'''.

On the layer of the Speaker’s cushions left,

Draw a circle.

Ensure that the Opacity value is set to 100

|-
|| '''Canvas''' Draw a circle

>>'''Fill>> '''Remove the fill'''

>>''' Scale >> Rotate
|| Go to '''Fill''' tab and remove the '''Fill'''.

Make sure that the '''Stroke''' option is selected in the '''Fill and stroke ''' tab.

Scale and rotate the circle as required.

|-
|| '''Canvas'''>> '''Edit'''

>> '''Duplicate>'''>>

select one of the duplicated circles

>> Scale and adjust >>

Select remaining one of the duplicated circles drag and adjust
|| To make the inside part of the speaker's cushion, adjust the circle as shown.

Go to '''Edit menu '''and click on '''Duplicate ''' to make a copy of the drawn circle.

Duplicate the drawn circle twice.

The duplicated circles are positioned in the same location as the drawn circle.

Select one of the duplicated circles.

Drag and adjust it as shown.

|-
|| '''Canvas >> Path >>

'''Click on '''Difference'''
|| Now, select the shifted circle and the remaining duplicated circle.

Go to the '''Path''' and click on '''Difference.'''

|-
|| '''Canvas''' >>
Duplicate the remaining one of the duplicated circle
>> Scale and adjust
|| The duplicated circles were used to create the inside part of the speaker's cushion.

Only the initial circle remains on the canvas.

To create the front part of the speaker's cushion.

Create a duplicate of the initial circle that is still on the canvas.

Scale and adjust as shown.

|-
|| '''Canvas''' >>

Duplicate the adjusted circle twice

>> Move and adjust one of the duplicated circles

>> Select the adjusted circle and the remaining duplicated circle.

|| Now, let us create the middle part of the speaker's cushion.

Duplicate the adjusted circle twice.

Move and adjust one of the duplicated circles as demonstrated.

Select the adjusted circle and the remaining duplicated circle.
|-
|| '''Path'''>> Click on '''Union'''
|| Go to '''Path''' and click on '''Union'''.

|-
|| '''Canvas'''>> ''' Editing nodes'''.
|| Adjust circles by editing the nodes as demonstrated.

|-
|| '''Canvas'''>> Duplicate the edited shape twice

>> Select one of the duplicated shape

>> Move and adjust as demonstrated.
|| To make the cushion's backside, duplicate the edited shape twice.

Select one of the duplicated shapes.

Move and adjust as demonstrated.
|-
||
|| To get the difference,

Please note:

The shape from which we want to get the difference has to be kept behind the current shape.

|-
|| '''Canvas ''' >>

Select edited shape and one of the duplicated shape

>>''' Path''' >> Click on''' Difference'''

|| Select the edited shape and the remaining duplicated shape.

Go to '''Path''' and click on''' Difference'''.

|-
|| '''Canvas''' >>

Duplicate the shape resulting from the difference.

'''>> Layers panel '''Create a new''' Layer '''named

'''Speaker cup Left >>

'''Select the '''Layer '''of the duplicated shape from the''' Layers panel'''

>>Drag and drop into the '''Layer''' of the''' Speaker cup Left'''

>>''' Canvas>>'''

adjust as shown >>
Duplicate the adjusted shape and edit it for the remaining part of the speaker’s cup.

|| To make the speaker’s cup, duplicate the shape resulting from the difference.

Create a new''' Layer '''named '''Speaker cup Left'''.

Select the '''Layer '''of the duplicated shape from the''' Layers panel'''.

Drag and drop into the '''Layer''' of the''' Speaker cup Left'''

Go to the '''Canvas''' and adjust as shown.

Duplicate the adjusted shape and edit it for the remaining part of the speaker’s cup.

|-
|| Cursor on the '''Canvas'''.
|| Now, add new layers to the right side speaker’s cushion and speaker’s cup.

Create the speaker’s cushion and speaker’s cup on the right side as before.
|-
|| '''Toolbar''' >> '''Bezier tool>>

Canvas'''>>Draw headband
||
Go to '''Toolbox'''. Select the '''Bezier tool'''.

Using the '''Bezier''' tool let us draw the various parts of the headband.

Users can draw the headband using the bezier tool as seen here.

The headband parts will look as shown.
|-
|| '''Layer panel >>

'''Select reference image >>

'''Canvas'''>>Move, scale and adjust >>

'''Fill and Stroke '''>>''' Opacity'''
|| After all the parts are drawn, select the reference image '''Layer'''.

Click on the lock icon to unlock the '''Layer'''.

Go to '''Canvas.'''

Move, scale and adjust the reference image.

Make sure to increase the opacity to 100 before adding colors.

|-
|| '''Canvas''' >>

Select shape one by one >>

Fill colors>>''' Layers panel'''

>> Arrange layers

|| Select the shapes of the speaker’s cushions, speaker’s cups, and headband one by one.

Fill the color by''' '''picking a suitable color from the reference image as shown'''.'''

Go to the '''Layers panel'''.

Arrange layers from the '''Layers panel''' while filling colors as demonstrated.

|-
|| '''Canvas''' >>

Select all parts of the drawing >>

'''Stroke paint''' >>Click on '''No paint

>> Canvas >> '''point towards the gap
|| Select all parts of the drawing

Go to the '''Stroke paint''' tab.

Click on '''No paint ''' to remove the outlines from drawing.

Check the gaps between the shapes and adjust them.
|-
|| '''Canvas''' >>

Fill the '''Linear Gradient''' using '''Gradient tool'''.
|| Select the shapes of the speaker’s cushion, speaker’s cup, and headband one by one.

And apply the gradient.

To do so, Select the '''Gradient tool''' option from the '''Toolbar'''.

And Choose the '''Create linear gradient '''option from the '''Tool controls bar.'''

Apply the gradient by choosing a suitable color from the reference image

Adjust the gradient as demonstrated.

You can use '''Linear gradient ''' or ''' Radial gradient ''' as per the requirement.

This method helps to create depth and gives 3D realistic drawing.
|-
|| '''Canvas'''
|| For more details, create shadows and highlights using the '''Bezier tool'''.

|-
|| '''FIll >> '''Increase '''Blur '''value

>> '''Layers panel >>

'''Hide reference layer by clicking on eye icon
|| Now, go to the '''Fill tab.'''

Increase the '''Blur '''value for merging two colors as needed.

Add more details as applicable.

To hide the reference image, go to the ''' Layers panel'''.

Click on the eye icon of the reference image '''Layer'''.
|-
|| '''Layers panel >>

'''Select all the layers '''

>> Object Menu >>

Group>>Layers panel

>> '''Double click on the''' Group layer '''

and rename it as''' Headphone'''
|| Select all the parts from the '''Layers panel '''at once.

Go to '''Object''' and click on '''Group.'''

Double click on the '''Group layer''' from the ''' Layers panel''' and rename it as '''Headphone.'''
|-
|| '''Filter >> Shadows and Glows

>>Drop Shadow>> Options >>

'''Adjust the parameters >>

'''Shadow type'''>>'''Outer

>>Preview>> '''click on the checkbox'''

>>''' '''Apply'''
|| Go to '''Filters menu'''.

Navigate to '''Shadows and Glows ''' and click on the '''Drop Shadow''' from the submenu.

'''Drop Shadow''' window opens'''.

Click on the '''Options '''and adjust the parameters as shown.

Make sure the '''Outer''' option is selected from the drop down menu of '''Shadow type'''.

To view the preview, click on the checkbox labeled "'''Live''' '''Preview'''".

Click on '''Apply'''. Close the window.
|-
|| '''Toolbar >> '''Select

'''Rectangle tool>>

Canvas>>'''Draw rectangle on the''' Canvas>> Layers panel>>

'''Rename the layer and arrange>>Select color from the
'''Palette'''

|| Select''' Rectangle tool '''from the '''Toolbox.'''

Draw a rectangle on the '''Canvas '''as demonstrated.

Rename the''' Layer''' as''' Background '''from the '''Layers panel'''.

Arrange the '''Layer '''behind the''' Layer''' of the head Phone.

Pick color from '''Palette '''as shown.

Now the 3D Drawing of a pair of headphones''' '''is ready.
|-
|| Point to the headphone
|| Similarly, you can create various other objects using this method.
|-
||'''Slide'''

'''Summary'''
|| This brings us to the end of this tutorial.

Let us summarize.

In this tutorial we have learnt to-

* Import a headphone’s picture into '''Inkscape'''
* Use '''Circle tool''', '''Difference '''and '''Union''' options to create speaker’s cups and cushions
* Use '''Bezier tool''' to create headband
* Create shadows and light using '''Gradient tool''' to bring depth to the drawing
* Create a 3D realistic drawing of a pair of headphones

|-
|| '''Slide'''

'''Assignment'''
|| Here is an assignment for you.
* Create the drawing of an ironbox from the image given in the Code files

|-
|| Completed assignment
|| Your completed assignment should look like this.
|-
||'''Slide'''

'''About Spoken Tutorial'''

|| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|'''Slide'''

'''Workshop'''

|| We conduct workshops using spoken tutorials and give certificates.

For more details, please write to us.
|-
||'''Slide'''

'''Spoken Tutorial Forum slide'''
||Do you have questions in THIS Spoken Tutorial?

Please visit this site

Choose the minute and second where you have the question

Explain your question briefly

The Spoken Tutorial project will ensure an answer

You will have to register to ask questions
|-
||'''Slide'''

'''Acknowledgment'''
|| Spoken Tutorial project was established by the Ministry of Education Government of India.
|-
||
|| This tutorial is contributed by Shital Joshi from IIT Bombay.

Thank you for joining.
|-
|}

Inkscape-Techniques-to-Create-Vector-Graphics/C2/3D-Drawing-of-a-Pair-of-Headphones/English

2024-05-31T06:36:18Z

Snehalathak:

'''Title of script: 3D Drawing of a Pair of Headphones'''

'''Author''': Shital

'''Keywords''': Inkscape, headphones, Gradient, Difference, Union, Bezier tool,3D Drawing of a pair of Headphones, Video tutorial.

{| border=1
|| '''Visual Cue'''
|| '''Narration'''
|-
|| '''Slide'''

'''Opening Slide'''
|| Welcome to this Spoken Tutorial on '''3D Drawing of a Pair of Headphones''' using '''Inkscape'''.
|-
|| '''Slide'''

'''Learning Objectives'''
|| In this tutorial we will,

* Import a headphone’s picture into '''Inkscape'''
* Use '''Circle tool''', '''Difference '''and '''Union''' options to create speaker’s cups and cushions
* Use '''Bezier tool''' to create a headband
* Create shadows and light using '''Gradient tool''' to bring depth to the drawing
* Create a 3D realistic drawing of a pair of Headphones

|-
|| '''Slide'''

'''System Requirement'''
|| To record this tutorial, I am using,
* '''Mac''' OS version 10.14.6
* '''Inkscape '''version 1.2.2

|-
|| '''Slide'''

'''Prerequisites'''

http://spoken-tutorial.org
|| To understand this tutorial, learner requires a good command of Inkscape tools.

For the prerequisite tutorials on '''Inkscape '''please visit this website.

|-
|| '''Slide'''

'''Code Files'''
|| The image used in this tutorial is given in the '''Code Files''' link.

Please download and extract the file.

Make a copy and then use it while practising.
|-
|| Open '''Inkscape'''
|| Let us open '''Inkscape.'''
|-
|| '''File '''>> '''Document Properties >>

Orientation ''' >> Select the ''''Landscape '''Orientation'''

Click on '''Close button(X)'''
|| Go to '''File ''' and click on '''Document Properties'''.

In the dialog box, select ''' Landscape Orientation'''.

Close the '''Document Properties '''dialog box.
|-
|| Go to '''File'''>> Click on '''Save'''.

In the Save dialog box type the filename as '''3D Drawing of a pair of Headphones.svg'''.

Click on '''Save''' button.
|| Let us now save the file.

Go to File. Click on '''Save'''.

In the '''Save''' dialog box type the filename as '''3D- Drawing-of-a-pair-of-Headphones.svg'''.

Click on '''Save''' button.

Please remember to save the file often while drawing.
|-
|| '''File '''>> '''Import >>

Select file to import '''>>

'''Desktop ''' >> Select the file >>

Click on '''Open '''.
|| Go to '''File '''and click on '''Import.'''

In the dialog box''' Select file to import'''.

Go to the location on your computer where the image is saved.

Select '''File''' and click on '''Open'''.
|-
|| '''Jpeg image bitmap import '''window opens.

Click on''' Ok''' >>

Close the dialog box >>

Point out imported image.

|| '''Jpeg bitmap image import '''window opens.

Click the '''OK ''' button to close the window.

Now, the image is loaded on the canvas.

Scale and adjust the reference image.
|-
|| Go to the '''Layers panel''' located on the right side of the interface.

>> Double click on the selected Layer >>

Rename the name as ‘Reference’

|| Go to the '''Layers panel''' located at the right side of the interface.

Double click on the selected Layer and rename the layer as ‘'''Reference'''’.

|-
|| Point out imported image >> '''Menu bar'''

>> Click on '''Object''' >>

Click on '''Fill and Stroke '''

||This image is for reference so you can decrease its '''Opacity'''.

To decrease the opacity, go to the''' Object''' menu on the '''Menu bar.'''

Click on ''' Fill and Stroke'''.
|-
|| '''Fill tab '''>> Change '''Opacity.'''
|| '''Fill and stroke '''window opens on the right side of the Interface.

Let us now adjust the '''Opacity'''.

Drag the opacity slider located at the bottom of the '''Fill and Stroke''' window.

|-
|| '''Layers panel''' >>

Click on lock icon.

|| The reference image must be retained as a reference as long as you work.

Go to the '''Layers''' panel.

Click the lock icon to lock the reference image layer.
|-
|| '''Slide'''

'''Add a Separate Layer'''
|| Please remember to add a separate layer for each part of the drawing.

Rename the layer with a proper name.

For example. '''Speaker’s cushion-Left''', '''Speaker’s cushion-Right''', '''Headband''' and others.

|-
|| '''Toolbar''' >> Select the '''Circle tool'''

>>'''Canvas'''>> Draw a circle

>> '''Fill''' >> '''Opacity''' Change the value to 100.

|| From the '''Toolbox''', Select the '''Circle tool'''.

On the layer of the Speaker’s cushions left,

Draw a circle.

Ensure that the Opacity value is set to 100

|-
|| '''Canvas''' Draw a circle

>>'''Fill>> '''Remove the fill'''

>>''' Scale >> Rotate
|| Go to '''Fill''' tab and remove the '''Fill'''.

Make sure that the '''Stroke''' option is selected in the '''Fill and stroke ''' tab.

Scale and rotate the circle as required.

|-
|| '''Canvas'''>> '''Edit'''

>> '''Duplicate>'''>>

select one of the duplicated circles

>> Scale and adjust >>

Select remaining one of the duplicated circles drag and adjust
|| To make the inside part of the speaker's cushion, adjust the circle as shown.

Go to '''Edit menu '''and click on '''Duplicate ''' to make a copy of the drawn circle.

Duplicate the drawn circle twice.

The duplicated circles are positioned in the same location as the drawn circle.

Select one of the duplicated circles.

Drag and adjust it as shown.

|-
|| '''Canvas >> Path >>

'''Click on '''Difference'''
|| Now, select the shifted circle and the remaining duplicated circle.

Go to the '''Path''' and click on '''Difference.'''

|-
|| '''Canvas''' >>
Duplicate the remaining one of the duplicated circle
>> Scale and adjust
|| The duplicated circles were used to create the inside part of the speaker's cushion.

Only the initial circle remains on the canvas.

To create the front part of the speaker's cushion.

Create a duplicate of the initial circle that is still on the canvas.

Scale and adjust as shown.

|-
|| '''Canvas''' >>

Duplicate the adjusted circle twice

>> Move and adjust one of the duplicated circles

>> Select the adjusted circle and the remaining duplicated circle.

|| Now, let us create the middle part of the speaker's cushion.

Duplicate the adjusted circle twice.

Move and adjust one of the duplicated circles as demonstrated.

Select the adjusted circle and the remaining duplicated circle.
|-
|| '''Path'''>> Click on '''Union'''
|| Go to '''Path''' and click on '''Union'''.

|-
|| '''Canvas'''>> ''' Editing nodes'''.
|| Adjust circles by editing the nodes as demonstrated.

|-
|| '''Canvas'''>> Duplicate the edited shape twice

>> Select one of the duplicated shape

>> Move and adjust as demonstrated.
|| To make the cushion's backside, duplicate the edited shape twice.

Select one of the duplicated shapes.

Move and adjust as demonstrated.
|-
||
|| To get the difference,

Please note:

The shape from which we want to get the difference has to be kept behind the current shape.

|-
|| '''Canvas ''' >>

Select edited shape and one of the duplicated shape

>>''' Path''' >> Click on''' Difference'''

|| Select the edited shape and the remaining duplicated shape.

Go to '''Path''' and click on''' Difference'''.

|-
|| '''Canvas''' >>

Duplicate the shape resulting from the difference.

'''>> Layers panel '''Create a new''' Layer '''named

'''Speaker cup Left >>

'''Select the '''Layer '''of the duplicated shape from the''' Layers panel'''

>>Drag and drop into the '''Layer''' of the''' Speaker cup Left'''

>>''' Canvas>>'''

adjust as shown >>
Duplicate the adjusted shape and edit it for the remaining part of the speaker’s cup.

|| To make the speaker’s cup, duplicate the shape resulting from the difference.

Create a new''' Layer '''named '''Speaker cup Left'''.

Select the '''Layer '''of the duplicated shape from the''' Layers panel'''.

Drag and drop into the '''Layer''' of the''' Speaker cup Left'''

Go to the '''Canvas''' and adjust as shown.

Duplicate the adjusted shape and edit it for the remaining part of the speaker’s cup.

|-
|| Cursor on the '''Canvas'''.
|| Now, add new layers to the right side speaker’s cushion and speaker’s cup.

Create the speaker’s cushion and speaker’s cup on the right side as before.
|-
|| '''Toolbar''' >> '''Bezier tool>>

Canvas'''>>Draw headband
||
Go to '''Toolbox'''. Select the '''Bezier tool'''.

Using the '''Bezier''' tool let us draw the various parts of the headband.

Users can draw the headband using the bezier tool as seen here.

The headband parts will look as shown.
|-
|| '''Layer panel >>

'''Select reference image >>

'''Canvas'''>>Move, scale and adjust >>

'''Fill and Stroke '''>>''' Opacity'''
|| After all the parts are drawn, select the reference image '''Layer'''.

Click on the lock icon to unlock the '''Layer'''.

Go to '''Canvas.'''

Move, scale and adjust the reference image.

Make sure to increase the opacity to 100 before adding colors.

|-
|| '''Canvas''' >>

Select shape one by one >>

Fill colors>>''' Layers panel'''

>> Arrange layers

|| Select the shapes of the speaker’s cushions, speaker’s cups, and headband one by one.

Fill the color by''' '''picking a suitable color from the reference image as shown'''.'''

Go to the '''Layers panel'''.

Arrange layers from the '''Layers panel''' while filling colors as demonstrated.

|-
|| '''Canvas''' >>

Select all parts of the drawing >>

'''Stroke paint''' >>Click on '''No paint

>> Canvas >> '''point towards the gap
|| Select all parts of the drawing

Go to the '''Stroke paint''' tab.

Click on '''No paint ''' to remove the outlines from drawing.

Check the gaps between the shapes and adjust them.
|-
|| '''Canvas''' >>

Fill the '''Linear Gradient''' using '''Gradient tool'''.
|| Select the shapes of the speaker’s cushion, speaker’s cup, and headband one by one.

And apply the gradient.

To do so, Select the '''Gradient tool''' option from the '''Toolbar'''.

And Choose the '''Create linear gradient '''option from the '''Tool controls bar.'''

Apply the gradient by choosing a suitable color from the reference image

Adjust the gradient as demonstrated.

You can use '''Linear gradient ''' or ''' Radial gradient ''' as per the requirement.

This method helps to create depth and gives 3D realistic drawing.
|-
|| '''Canvas'''
|| For more details, create shadows and highlights using the '''Bezier tool'''.

|-
|| '''FIll >> '''Increase '''Blur '''value

>> '''Layers panel >>

'''Hide reference layer by clicking on eye icon
|| Now, go to the '''Fill tab.'''

Increase the '''Blur '''value for merging two colors as needed.

Add more details as applicable.

To hide the reference image, go to the ''' Layers panel'''

Click on the eye icon of the reference image '''Layer'''.
|-
|| '''Layers panel >>

'''Select all the layers '''

>> Object Menu >>

Group>>Layers panel

>> '''Double click on the''' Group layer '''

and rename it as''' Headphone'''
|| Select all the layers from the '''Layers panel '''at once.

Go to '''Object''' and click on '''Group.'''

Double click on the '''Group layer''' from the ''' Layers panel''' and rename it as '''Headphone.'''
|-
|| '''Filter >> Shadows and Glows

>>Drop Shadow>> Options >>

'''Adjust the parameters >>

'''Shadow type'''>>'''Outer

>>Preview>> '''click on the checkbox'''

>>''' '''Apply'''
|| Go to '''Filters menu'''.

Navigate to '''Shadows and Glows ''' and click on the '''Drop Shadow''' from the submenu.

'''Drop Shadow''' window opens'''.

Click on the '''Options '''and adjust the parameters as shown.

Make sure the '''Outer''' option is selected from the drop down menu of '''Shadow type'''.

To view the preview, click on the checkbox labeled "'''Live''' '''Preview'''".

Click on '''Apply'''. Close the window.
|-
|| '''Toolbar >> '''Select

'''Rectangle tool>>

Canvas>>'''Draw rectangle on the''' Canvas>> Layers panel>>

'''Rename the layer and arrange>>Select color from the
'''Palette'''

|| Select''' Rectangle tool '''from the '''Toolbox.'''

Draw a rectangle on the '''Canvas '''as demonstrated.

Rename the''' Layer''' as''' Background '''from the '''Layers panel'''.

Arrange the '''Layer '''behind the''' Layer''' of the head Phone.

Pick color from '''Palette '''as shown.

Now the 3D Drawing of a pair of headphones''' '''is ready.
|-
|| Point to the headphone
|| Similarly, you can create various other objects using this method.
|-
||'''Slide'''

'''Summary'''
|| This brings us to the end of this tutorial.

Let us summarize.

In this tutorial we have learnt to-

* Import a headphone’s picture into '''Inkscape'''
* Use '''Circle tool''', '''Difference '''and '''Union''' options to create speaker’s cups and cushions
* Use '''Bezier tool''' to create headband
* Create shadows and light using '''Gradient tool''' to bring depth to the drawing
* Create a 3D realistic drawing of a pair of headphones

|-
|| '''Slide'''

'''Assignment'''
|| Here is an assignment for you.
* Create the drawing of an ironbox from the image given in the Code files

|-
|| Completed assignment
|| Your completed assignment should look like this.
|-
||'''Slide'''

'''About Spoken Tutorial'''

|| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|'''Slide'''

'''Workshop'''

|| We conduct workshops using spoken tutorials and give certificates.

For more details, please write to us.
|-
||'''Slide'''

'''Spoken Tutorial Forum slide'''
||Do you have questions in THIS Spoken Tutorial?

Please visit this site

Choose the minute and second where you have the question

Explain your question briefly

The Spoken Tutorial project will ensure an answer

You will have to register to ask questions
|-
||'''Slide'''

'''Acknowledgment'''
|| Spoken Tutorial project was established by the Ministry of Education Government of India.
|-
||
|| This tutorial is contributed by Shital Joshi from IIT Bombay.

Thank you for joining.
|-
|}

ORCA---Computational-Chemistry/C2/Run-an-Input--File/English

2024-05-01T10:59:53Z

Snehalathak:

'''Title of the script''': '''Run Orca Input file '''

'''Author: '''Arup Sarkar, Raj Singh and Madhuri Ganapathi

'''Keywords: '''ORCA, Avogadro, water, xyz file, xyz coordinates, input file, output file, bond length, bond angle, video tutorial.

{| border=1
|-
||'''Visual Cue'''
||'''Narration'''
|-
|| '''Slide Number 1 '''

'''Title slide '''
|| Welcome to this spoken tutorial on

'''Run an Input File '''using '''ORCA.'''
|-
|| '''Slide Number 2 '''

'''Learning Objectives'''

|| In this tutorial, we will learn to,
* Run an input file in the '''ORCA''' environment.
* Generate an output file.
* Compare the bond length and bond angle before and after optimization in '''ORCA'''.
* Analyse the generated output

|-
|| '''Slide Number 3'''

'''System Requirement'''
|| To record this tutorial, I am using;

'''Ubuntu Linux''' OS version 20.04

'''ORCA''' version 5.0.4

'''Gedit''' text editor version 3.36.2

'''Avogadro''' version 1.2.0

|-
|| '''Slide Number 4'''

'''Pre-requisites'''

'''https://spoken-tutorial.org'''

|| To follow this tutorial,

Learner, should be familiar with '''Avogadro software '''and

Learner, should have installed '''ORCA''' version 5.0.4

If not please access the relevant tutorials from this website.
|-
|| '''Slide Number 5'''

'''Code Files'''

|| The files used in this tutorial are provided in the Code files link.

Please download and extract the files.

Make a copy and then use them while practising.
|-
|| Cursor in the ''' Home folder'''.

Double-click to open the '''Water folder'''.

|| Let us go to the '''Home directory ''' and open the ''' water folder'''.
|-
|| Point to''' water.xyz '''and '''water.inp '''file in the''' water folder.'''
|| Learners please note:

The '''water''' folder was created earlier while practising the prerequisite tutorial.

Please refer to the prerequisite tutorial for more information.
|-
|| Press Ctrl + A to select the files.

Right-click >> copy

Right-click >> paste,

|| Let us make a copy of the files present in the '''water folder'''.

Rename the copied files as '''waterA.xyz''' and '''waterA.inp'''.

Users can rename the files as desired.

This helps to compare the '''xyz ''' coordinates after the input file is run using '''ORCA'''.

|-
|| Right-click and select''' Open With Text Editor.'''
|| Now let’s open the '''water.inp''' file using a text editor.

Windows users may use a ''' notepad''' or any other text editor to open the '''input''' file.

|-
|| Point to the '''xyz '''coordinates of the molecule.
|| Notice the '''xyz ''' coordinates of the molecule.

They are obtained after '''auto optimization '''of the molecule in '''Avogadro'''.

|-
|| Point to # and line next to it.
|| The lines after the''' hash(#) ''' symbol will be treated as comments.

'''ORCA ''' will not execute these lines.

So skip the lines.
|-
|| Point to line '''! RHF OPT def2-SVP '''

Point to !.

|| The program code starts with an exclamatory(!) mark.
|-
|| Point to '''RHF'''

Point to '''def2-SVP '''

Point to '''OPT'''

|| Here '''RHF ''' is the''' Restricted Hartree Fock ''' method.

Using this method we will run a geometry optimization of water molecule.

'''def2-SVP''' is the '''Basis set ''' in ''' ORCA'''.

The '''OPT '''keyword is used to optimize the molecule in '''ORCA'''.
|-
|| Point to * xyz 0 1

Point to the asterisk at the start and end.
|| Here '''xyz '''specifies the coordinates of the molecule in '''Angstrom''' units.

0 is the charge and

1 is the spin multiplicity(2S+1)

The coordinates should start and end with an '''asterisk''' (*).
|-
|| Point to the '''Close''' button.

Click the Close button.
|| All the command lines are correct.

You can close the input file.
|-
|| '''Run the Input File in ORCA'''
|| Now we will run the '''water.inp''' file in the '''ORCA '''environment.

|-
|| Point to the '''ORCA '''file in the '''Home''' folder.

Double-click to open the '''orca '''folder.
|| I have already installed and extracted the '''ORCA 5.0.4''' file to my '''Home''' directory.

I will open the '''orca '''folder.
|-
|| Move the cursor on the files in the folder.

Point to the '''orca program.'''

|| Here, all the files are already compiled and are in executable format.

All calculations will run using the '''orca '''executable file.
|-
|| Show the '''water ''' and ''' orca ''' directories are in the home directory.
|| Both '''orca''' and '''water ''' directories are in the '''Home directory'''.

|-
||Press '''Ctrl + Alt + T ''' keys together to open the terminal.
|| Open the terminal by pressing '''Ctrl''', '''Alt ''' and''' T ''' keys together.

|-
||
|| Let’s create an '''alias''' for the path to fetch the '''orca''' program.
|-
|| Type '''gedit .bashrc'''

>> press '''Enter.'''

|| Type '''gedit space .bashrc''' and press Enter to edit the '''bashrc '''file.

The file opens.
|-
|| Show the '''alias''' command in the '''.bashrc file'''.
|| In the file, I have added the path in the '''alias''' command to fetch '''orca.'''

Users please the type file path as per your file location.
|-
|| Click on the X button to close the file.
|| Close the '''.bashrc''' file.

|-
|| Type '''source .bashrc''' at the prompt.

Press '''Enter'''.

||Let us go back to the terminal, to source the file.

At the prompt type, '''source space .bashrc '''and Press '''Enter'''.

From now on, instead of typing the full path just type '''orca''' at the prompt.
|-
|| Cursor on the terminal.
|| Now we will run the input file in '''ORCA'''.

|-
|| Type '''orca space ~/Water/water.inp'''

Highlight file location.
|| Type '''orca '''space ~/'''water/water.inp''', as we are in the '''water '''folder.

|-
||'''Type > ~/Water/water.out'''

'''Press Enter '''

|| Please give a '''space '''after typing the path of the input file.

Now type greater''' '''than('''>''') sign.

Here greater''' '''than('''>''') sign is used to channel the output to the same folder.

Press''' space''' bar again

To save the output file in the current directory, type '''~/water/water.out'''

This will direct the output to a text file.

Please type the file path as per your file location.

Press '''Enter''' to run the command.

|-
|| Point to the files in the '''water''' folder.

Open the '''water''' folder along with the terminal to see the files.
|| Observe that some temporary files are generated in the folder.

These files are generated as the '''input''' file runs in '''ORCA'''.

The temporary files are removed after output files are generated.

The generation of the output takes a few seconds.

|-
|| Double click on the '''water.out''' file.

Scroll down to show the output.

Point to the '''FINAL SINGLE POINT ENERGY '''

'''-75.961333016443 Eh'''

|| Double click on the '''water.out'''

file to open it.

Scroll down the file to see the output.

Here is the final single point energy after the '''Hartree Fock optimization'''.

This number may vary a little for the learners.

Single point energy is the lowest energy solution to Schrödinger's equation.
|-
|| Show the Converged cycles.
|| When the input file runs in''' ORCA''' it creates different converge cycles.

Then optimises the structure.

So the''' xyz '''coordinates change after the optimisation is done.
|-
|| Click on the X button to close the file.
|| Let us now close the file.
|-
|| Cursor on '''water.xyz '''file.

Double click on the files to open them.

Click on '''water.xyz''' file.

Point to the coordinates.
|| Let’s open the files '''water.xyz''' and''' waterA.xyz'''.

Here we can compare the values of the xyz coordinates in the '''xyz''' files.

Observe the change in values of XYZ coordinates.
|-
|| Point to the coordinates.
|| The coordinates have changed after the structure converged in '''orca'''.

This indicates that the structure is better converged in the ORCA environment.
|-
||Click on the X button.
|| Let us close the files.
|-
|| Point to the file.

Right-click on the file, select the option '''Open With Other Application '''

|| Let us open the '''xyz''' file in''' Avogadro'''.

Right-click on '''water.xyz file. '''

Select '''Open With Other Application '''option.

|-
|| Point to the dialog box.

From the '''Recommended Applications '''select '''Avogadro.'''

Click on the '''Selec'''t''' '''button at the top right corner of the dialog box.

Point to the '''water '''molecule in the '''Avogadro''' panel.
|| '''Select Application''' dialog box opens.

From the '''Recommended Applications '''select '''Avogadro.'''

Click on '''Selec'''t''' '''button at the top right corner of the dialog box.

'''Water '''molecule is loaded in the panel.
|-
|| Click on '''Click to Measure''' tool on the toolbar.

Click on Hydrogen and then on Oxygen atom to measure the bond length.

Point to the bond length at the bottom.

Show text box: with bond length after auto optimization in '''Avogadro'''.

|| Now click the '''Click to Measure''' tool on the toolbar.

Click on Hydrogen and then on click oxygen atom to measure the bond length.

Observe that the bond length is 0.945 A0

This value is close to the experimental value suggested in literature.

In the prerequisite tutorial we have determined the bond length as 0.969 A0.

This value was obtained after auto optimization of the structure in Avogadro.

|-
||Click on Second hydrogen atom.

Point to the bond angle at the bottom left.

Show text box: with bond angle after auto optimization in Avogadro.
|| Click on the next hydrogen atom to measure the bond angle.

Observe that the bond angle is 105.1 degrees

This value is close to the experimental value suggested in literature.

In the prerequisite tutorial we have determined the bond angle as 104.0 degrees.

This value was obtained after auto optimization of the structure in Avogadro.

|-
||Click on the X button to close.
|| Close the Avogadro interface.
|-
||
||Now we will analyse the output.
|-
|| Right-click on the water folder, select the option Open in Terminal.

Point to the folder in the terminal.

||Right-click on the water folder and select the option '''Open in Terminal'''.

Folder opens in the terminal.
|-
|| Type '''ls''' at the prompt.

Press '''Enter'''

Point to the list of files.

Point to '''water.out'''

|| Type '''ls '''at the prompt and Press '''Enter '''to see the list files.

Here we have the '''water.out''' file.

|-
|| Point to '''water.out.'''

Type '''vi <space> water.out '''and press '''Enter.'''

Point to the output.

Point to the cursor.

|| Now let us open this file using the '''vi editor.'''

Type '''vi <space> water.out '''and press '''Enter.'''

Output is shown on the terminal.

Observe that the cursor is at the top left corner.
|-
|| Press Shift + G.
|| Press '''Shift '''and''' G''' keys togther to go to the bottom of the terminal output.
|-
|| Point to time.
|| Here we can see the time taken to generate the output in the '''orca''' environment.

|-
||Type '''?Item''', press Enter.

Point to''' Item''' keyword.

|| Type '''?Item ''' and press '''Enter'''.

It searches for the '''Item''' keyword.

In this section, the file has converged to show the geometry optimization.

|-
||Type '''?TOTAL''' and press '''Enter'''.

Point to total '''SCF''' energy.

||Type '''?TOTAL''' all in capital letters and press '''Enter'''.

Search shows the total '''SCF''' energy.

Here '''SCF''' is a '''self-consistent field ''' method to calculate energy.
|-
|| Type '''?FINAL ''' and press '''Enter'''.

Point to the Final single point energy.
|| Type '''?FINAL''' all in capital letters and press Enter.

Search shows the '''Final Single Point '''energy after optimization.

|-
|| Press :q to quit the process.

Type cd ..

|| Press colonq(''':q)''' and press Enter to quit the process.

Type '''cd <space> <dot> <dot> (cd ..)''' to go back to the''' Home folder'''.

|-
||
|| With this, we come to the end of this tutorial.

Let us summarize.

|-
|| '''Slide Number 6'''

'''Summary'''
|| In this tutorial, we have
* Ran an input file in the ''' ORCA''' environment using the terminal.
* Generated an output file.
* Compared the bond length and bond angle before and after optimization in '''ORCA'''.
* Analysed the generated output

|-
|| '''Slide Number 7 + 8'''

'''Assignment'''

|| As an assignment,

* Open the input files of '''cyclohexane''' and '''benzene''' generated in the previous assignment
* Run the input files in the '''ORCA''' environment using the terminal
* Generate the output files.
* Compare the bond lengths and bond angles before and after optimization in '''ORCA'''.

|-
|| '''Slide Number 9'''

'''Spoken Tutorial project'''
|| The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.
|-
|| '''Slide number 10'''

'''Spoken Tutorial workshop'''
|| The spoken tutorial project team conducts workshops and gives certificates.

For more details, please write to us.
|-
|| '''Slide Number 11'''

'''Spoken Tutorial forum'''
|| Please post your timed queries in this forum.
|-
|| '''Slide number 12'''

'''Acknowledgement'''
|| '''Spoken Tutorial Project''' was established by the Ministry of Education Government of India.
|-
||Thank you
|| The tutorial is contributed by Arup Sarkar, Raj Singh and Madhuri Ganapathi from FOSSEE, IIT Bombay.

Thank you for joining.
|-
|}

AutoDock4/C2/Running-AutoDock/English

2024-01-18T05:48:56Z

Snehalathak:

'''Title of script''': '''Running AutoDock'''

'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''

'''Keywords: Autodock4, docking, docking parameters, genetic algorithm, dpf file, pdbqt files, dlg file, video tutorial.'''

{|border =1

|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Running AutoDock'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to

Open the '''PDBQT''' files for receptor and ligand for docking on the '''ADT''' interface

Perform docking using default docking parameters

Save the output as '''.dpf''' file

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| Run AutoDock

Open the .dlg file to make sure the autodock run is successfully completed.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using,

'''Ubuntu Linux''' OS version 20.04

AutoDockTools version 1.5.7

gedit version 3.36.2
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on '''AutoDock Tools''' interface
|-
|| '''Slide number 6'''

'''Code Files'''

|| The input files required for this tutorial are available in the '''Code files''' link.

Please download and extract the files.

|-
|| '''Slide number 7'''

'''Code Files'''

|| Save the input files in your home directory or working directory

Make a copy of all the files and then use them for practising.

|-
|| Cursor on ADT interface.
|| Here I have opened ADT interface.

|-
|| Click on '''Docking''' on the toolbar.

Select '''Macromolecule''' from the dropdown, then click '''Set Rigid Filename.'''

Cursor on the panel.

Select '''2vta.pdbqt''' from the list of files. Click on the '''Open '''button.

|| Click on the '''Docking''' tool on the menu bar.

Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename'''.

'''PDBQT Macromolcule File '''window opens.

Select '''2vta.pdbqt''' from the list of files and click on the '''Open ''' button.

|-
|| click on '''Docking''', from the dropdown choose '''Ligand,''' and select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

Cursor on the''' AutoDpf4 Ligand Parameters '''pop-up window.

Click on the '''Accept '''button in the pop-up.

|| Click on '''Docking''' again, from the dropdown choose '''Ligand,''' select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

A pop up window '''AutoDpf4 Ligand Parameters''' appears.

Read the information about the ligand.

Some default parameters are selected, leave them as such.

Click on the '''Accept ''' button in the pop-up.

The pop up window closes
|-
|| Click Docking >> Search Parameters >> Genetic Algorithm.

Cursor on '''Genetic Algorithm Parameters''' window.

Click the '''Accept''' button.

|| Click on '''Docking''' again, from the dropdown choose '''Search Parameters'''.

From the sub-menu select '''Genetic Algorithm'''.

'''Genetic Algorithm Parameters''' window opens.

You will notice that all the fields are auto populated.

We will leave the default parameters as such and click on ''' Accept''' button.
|-
|| Click Docking >> Docking Parameters.

Cursor on the '''Set Docking Run Options '''window.

Click the '''Accept '''button.

|| Next click again on '''Docking''' and from the dropdown choose '''Docking Parameters'''.

'''Set Docking Run Options ''' window opens.

Again you will notice that all the fields are auto populated.

We will leave them as such and click on ''' Accept''' button.

|-
|| Click Docking >> Output >> Lamarckian GA(4.2).

'''Autodock4.2 GALS Docking Parameter Output File''' window opens.

Type the file name in the File name field as''' 2vta.dpf'''.

The Files of type field is auto populated as '''dpf '''file.

Click on '''Save''' Button.

|| To save all the parameters as a single docking file; click '''Docking''' again.

Choose the '''Output''' option from the dropdown.

From the sub-menu choose '''Lamarckian GA(4.2)'''.

'''Autodock4.2 GALS Docking Parameter Output File''' dialog box opens.

Type the file name in the '''File name '''field as ''' 2vta.dpf'''.

The Files of type field is chosen as '''dpf''' file.

Click on '''Save''' Button.

|-
|| Click Run >> Run AutoDock.

Cursor on '''Run AutoDock''' pop-up.

|| Next, Click on '''Run''', Choose '''Run AutoDock'''.

'''Run AutoDock''' pop-up opens.

|-
|| Cursor on '''Run AutoDock''' pop-up.
|| Here you will again need to set the '''Program Pathname ''' and '''Parameter Filename'''.

For me '''Program Pathname''' is already auto populated.

Hence I will leave it as such.

Windows users may click on the '''Browse''' button and fill the path for the '''autodock4.exe file'''.
|-
|| Click on the '''Browse''' button next to the '''Parameter Filename '''field.

From the pop-up window, choose '''2vta.dpf''' from the home folder.

|| '''Parameter Filename ''' is also auto populated as '''2vta.dpf.'''

Click on the '''Browse''' button next to the field.

From the pop-up window, I will choose '''2vta.dpf''' from the Home folder.

Click on the '''Open''' button in the pop-up window.

Now the empty field next to '''Log Filename''' will automatically be populated as '''2vta.dlg'''.
|-
|| Cursor on the cmd field.
|| Here you may also find the command line if you prefer to use the terminal to run '''autodock4'''.
|-
|| Click on the '''Launch''' button.

Cursor on '''Autodock process Manager''' popup.
|| Click on the '''Launch''' button to run autodock4.

A pop-up titled '''Autodock Process Manager''' will appear.

The process time depends on the '''parameter values''' you have set.

This will take 10 to 20 seconds.

The pop-up will automatically close when the process ends.

|-
|| Cursor on the panel.
|| Viewers please note:

If the popup appears and closes quickly within 1 or 2 seconds, an error has likely occurred.

If this happens, check your parameters and '''run '''the '''autodock''' again.
|-
|| Cursor on the home folder .

Cursor on output file '''2vta.dlg'''.

Right-click on '''2vta.dlg''' and open it using the text editor.
|| Open the''' home '''folder.

The output file '''2vta.dlg''' will be saved in the home folder.

We need to open the '''dlg '''file and check the last line to make sure '''autodock''' is successfully completed.

I will right-click and open the file using the text editor.

|-
|| Cursor on '''2vta.dlg '''document.

Scroll to the last line in the document.

Cursor on '''Autodock4 Successful Completion.'''

|| The file opened in gedit for me.

Scroll to the last line in the document.

Here you will see, '''Autodock4: Successful Completion'''.

Close the text file and close the home folder..

This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary'''
|| Let us summarize.

In this tutorial, we have,

Opened the PDBQT files for receptor and ligand for docking on ADT interface

Performed docking using default docking parameters

|-
|| '''Slide Number 9'''

'''Summary'''
|| Saved the output as .dpf file

Ran AutoDock

Opened the .dlg file to make sure the autodock run is successfully completed

|-
|| '''Slide Number 10'''

'''Assignment'''
|| As an assignment,

Run autodock for the example 1DWD, given in the '''Examples '''folder in the Downloads page.

|-
|| '''Slide''' '''Number 11'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 113'''

'''Forum'''
||
* Please post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgement '''
||Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
|| '''Slide Number 14'''

'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}

AutoDock4/C2/Running-AutoDock/English

2024-01-18T05:47:24Z

Snehalathak:

'''Title of script''': '''Running AutoDock'''

'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''

'''Keywords: Autodock4, docking, docking parameters, genetic algorithm, dpf file, pdbqt files, dlg file, video tutorial.'''

{|border =1

|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Running AutoDock'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to

Open the '''PDBQT''' files for receptor and ligand for docking on the '''ADT''' interface

Perform docking using default docking parameters

Save the output as '''.dpf''' file.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| Run AutoDock

Open the .dlg file to make sure the autodock run is successfully completed.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using,

'''Ubuntu Linux''' OS version 20.04

AutoDockTools version 1.5.7

gedit version 3.36.2
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on '''AutoDock Tools''' interface
|-
|| '''Slide number 6'''

'''Code Files'''

|| The input files required for this tutorial are available in the '''Code files''' link.

Please download and extract the files.

|-
|| '''Slide number 7'''

'''Code Files'''

|| Save the input files in your home directory or working directory

Make a copy of all the files and then use them for practising.

|-
|| Cursor on ADT interface.
|| Here I have opened ADT interface.

|-
|| Click on '''Docking''' on the toolbar.

Select '''Macromolecule''' from the dropdown, then click '''Set Rigid Filename.'''

Cursor on the panel.

Select '''2vta.pdbqt''' from the list of files. Click on the '''Open '''button.

|| Click on the '''Docking''' tool on the menu bar.

Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename'''.

'''PDBQT Macromolcule File '''window opens.

Select '''2vta.pdbqt''' from the list of files and click on the '''Open ''' button.

|-
|| click on '''Docking''', from the dropdown choose '''Ligand,''' and select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

Cursor on the''' AutoDpf4 Ligand Parameters '''pop-up window.

Click on the '''Accept '''button in the pop-up.

|| Click on '''Docking''' again, from the dropdown choose '''Ligand,''' select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

A pop up window '''AutoDpf4 Ligand Parameters''' appears.

Read the information about the ligand.

Some default parameters are selected, leave them as such.

Click on the '''Accept ''' button in the pop-up.

The pop up window closes
|-
|| Click Docking >> Search Parameters >> Genetic Algorithm.

Cursor on '''Genetic Algorithm Parameters''' window.

Click the '''Accept''' button.

|| Click on '''Docking''' again, from the dropdown choose '''Search Parameters'''.

From the sub-menu select '''Genetic Algorithm'''.

'''Genetic Algorithm Parameters''' window opens.

You will notice that all the fields are auto populated.

We will leave the default parameters as such and click on ''' Accept''' button.
|-
|| Click Docking >> Docking Parameters.

Cursor on the '''Set Docking Run Options '''window.

Click the '''Accept '''button.

|| Next click again on '''Docking''' and from the dropdown choose '''Docking Parameters'''.

'''Set Docking Run Options ''' window opens.

Again you will notice that all the fields are auto populated.

We will leave them as such and click on ''' Accept''' button.

|-
|| Click Docking >> Output >> Lamarckian GA(4.2).

'''Autodock4.2 GALS Docking Parameter Output File''' window opens.

Type the file name in the File name field as''' 2vta.dpf'''.

The Files of type field is auto populated as '''dpf '''file.

Click on '''Save''' Button.

|| To save all the parameters as a single docking file; click '''Docking''' again.

Choose the '''Output''' option from the dropdown.

From the sub-menu choose '''Lamarckian GA(4.2)'''.

'''Autodock4.2 GALS Docking Parameter Output File''' dialog box opens.

Type the file name in the '''File name '''field as ''' 2vta.dpf'''.

The Files of type field is chosen as '''dpf''' file.

Click on '''Save''' Button.

|-
|| Click Run >> Run AutoDock.

Cursor on '''Run AutoDock''' pop-up.

|| Next, Click on '''Run''', Choose '''Run AutoDock'''.

'''Run AutoDock''' pop-up opens.

|-
|| Cursor on '''Run AutoDock''' pop-up.
|| Here you will again need to set the '''Program Pathname ''' and '''Parameter Filename'''.

For me '''Program Pathname''' is already auto populated.

Hence I will leave it as such.

Windows users may click on the '''Browse''' button and fill the path for the '''autodock4.exe file'''.
|-
|| Click on the '''Browse''' button next to the '''Parameter Filename '''field.

From the pop-up window, choose '''2vta.dpf''' from the home folder.

|| '''Parameter Filename ''' is also auto populated as '''2vta.dpf.'''

Click on the '''Browse''' button next to the field.

From the pop-up window, I will choose '''2vta.dpf''' from the Home folder.

Click on the '''Open''' button in the pop-up window.

Now the empty field next to '''Log Filename''' will automatically be populated as '''2vta.dlg'''.
|-
|| Cursor on the cmd field.
|| Here you may also find the command line if you prefer to use the terminal to run '''autodock4'''.
|-
|| Click on the '''Launch''' button.

Cursor on '''Autodock process Manager''' popup.
|| Click on the '''Launch''' button to run autodock4.

A pop-up titled '''Autodock Process Manager''' will appear.

The process time depends on the '''parameter values''' you have set.

This will take 10 to 20 seconds.

The pop-up will automatically close when the process ends.

|-
|| Cursor on the panel.
|| Viewers please note:

If the popup appears and closes quickly within 1 or 2 seconds, an error has likely occurred.

If this happens, check your parameters and '''run '''the '''autodock''' again.
|-
|| Cursor on the home folder .

Cursor on output file '''2vta.dlg'''.

Right-click on '''2vta.dlg''' and open it using the text editor.
|| Open the''' home '''folder.

The output file '''2vta.dlg''' will be saved in the home folder.

We need to open the '''dlg '''file and check the last line to make sure '''autodock''' is successfully completed.

I will right-click and open the file using the text editor.

|-
|| Cursor on '''2vta.dlg '''document.

Scroll to the last line in the document.

Cursor on '''Autodock4 Successful Completion.'''

|| The file opened in gedit for me.

Scroll to the last line in the document.

Here you will see, '''Autodock4: Successful Completion'''.

Close the text file and close the home folder..

This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary'''
|| Let us summarize.

In this tutorial, we have,

Opened the PDBQT files for receptor and ligand for docking on ADT interface

Performed docking using default docking parameters

|-
|| '''Slide Number 9'''

'''Summary'''
|| Saved the output as .dpf file

Ran AutoDock

Opened the .dlg file to make sure the autodock run is successfully completed

|-
|| '''Slide Number 10'''

'''Assignment'''
|| As an assignment,

Run autodock for the example 1DWD, given in the '''Examples '''folder in the Downloads page.

|-
|| '''Slide''' '''Number 11'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 113'''

'''Forum'''
||
* Please post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgement '''
||Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
|| '''Slide Number 14'''

'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}

AutoDock4/C2/Running-AutoDock/English

2024-01-18T05:35:34Z

Snehalathak:

'''Title of script''': '''Running AutoDock'''

'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''

'''Keywords: Autodock4, docking, docking parameters, genetic algorithm, dpf file, pdbqt files, dlg file, video tutorial.'''

{|border =1

|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Running AutoDock'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to

Open the '''PDBQT''' files for receptor and ligand for docking on the '''ADT''' interface

Perform docking using default docking parameters

Save the output as '''.dpf''' file.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| Run AutoDock

Open the .dlg file to make sure the autodock run is successfully completed.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using,

'''Ubuntu Linux''' OS version 20.04

AutoDockTools version 1.5.7

gedit v3.36.2
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial learner should be familiar with,

topics in basic bioinformatics

basic operations on '''AutoDock Tools''' interface
|-
|| '''Slide number 6'''

'''Code Files'''

|| The input files required for this tutorial are available in the '''Code files''' link.

Please download and extract the files.

|-
|| '''Slide number 7'''

'''Code Files'''

|| Save the input files in your home directory or working directory

Make a copy of all the files and then use them for practising.

|-
|| Cursor on ADT interface.
|| Here I have opened ADT interface.

|-
|| Click on '''Docking''' on the toolbar.

Select '''Macromolecule''' from the dropdown, then click '''Set Rigid Filename.'''

Cursor on the panel.

Select '''2vta.pdbqt''' from the list of files. Click on the '''Open '''button.

|| Click on the '''Docking''' tool on the menu bar.

Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename'''.

'''PDBQT Macromolcule File '''window opens.

Select '''2vta.pdbqt''' from the list of files and click on the '''Open ''' button.

|-
|| click on '''Docking''', from the dropdown choose '''Ligand,''' select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

Cursor on the''' AutoDpf4 Ligand Parameters '''pop-up window.

Click on the '''Accept '''button in the pop-up.

|| Click on '''Docking''' again, from the dropdown choose '''Ligand,''' select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

A pop up window '''AutoDpf4 Ligand Parameters''' appears.

Read the information about the ligand.

Some default parameters are selected, leave them as such.

Click on the '''Accept ''' button in the pop-up.

The pop up window closes
|-
|| Click Docking >> Search Parameters >> Genetic Algorithm.

Cursor on '''Genetic Algorithm Parameters''' window.

Click the '''Accept''' button.

|| Click on '''Docking''' again, from the dropdown choose '''Search Parameters'''.

From the sub-menu select '''Genetic Algorithm'''.

'''Genetic Algorithm Parameters''' window opens.

You will notice that all the fields are auto populated.

We will leave the default parameters as such and click on ''' Accept''' button.
|-
|| Click Docking >> Docking Parameters.

Cursor on the '''Set Docking Run Options '''window.

Click the '''Accept '''button.

|| Next click again on '''Docking''' and from the dropdown choose '''Docking Parameters'''.

'''Set Docking Run Options ''' window opens.

Again you will notice that all the fields are auto populated.

We will leave them as such and click on ''' Accept''' button.

|-
|| Click Docking >> Output >> Lamarckian GA(4.2).

'''Autodock4.2 GALS Docking Parameter Output File''' window opens.

Type the file name in the File name field as''' 2vta.dpf'''.

The Files of type field is auto populated as '''dpf '''file.

Click on '''Save''' Button.

|| To save all the parameters as a single docking file; click '''Docking''' again.

Choose the '''Output''' option from the dropdown.

From the sub-menu choose '''Lamarckian GA(4.2)'''.

'''Autodock4.2 GALS Docking Parameter Output File''' dialog box opens.

Type the file name in the '''File name '''field as ''' 2vta.dpf'''.

The Files of type field is chosen as '''dpf''' file.

Click on '''Save''' Button.

|-
|| Click Run >> Run AutoDock.

Cursor on '''Run AutoDock''' pop-up.

|| Next, Click on '''Run''', Choose '''Run AutoDock'''.

'''Run AutoDock''' pop-up opens.

|-
|| Cursor on '''Run AutoDock''' pop-up.
|| Here you will again need to set the '''Program Pathname ''' and '''Parameter Filename'''.

For me '''Program Pathname''' is already auto populated.

Hence I will leave it as such.

Windows users may click on the '''Browse''' button and fill the path for the '''autodock4.exe file'''.
|-
|| Click on the '''Browse''' button next to the '''Parameter Filename '''field.

From the pop-up window, choose '''2vta.dpf''' from the home folder.

|| '''Parameter Filename ''' is also auto populated as '''2vta.dpf.'''

Click on the '''Browse''' button next to the field.

From the pop-up window, I will choose '''2vta.dpf''' from the Home folder.

Click on the '''Open''' button in the pop-up window.

Now the empty field next to '''Log Filename''' will automatically be populated as '''2vta.dlg'''.
|-
|| Cursor on the cmd field.
|| Here you may also find the command line if you prefer to use the terminal to run '''autodock4'''.
|-
|| Click on the '''Launch''' button.

Cursor on '''Autodock process Manager''' popup.
|| Click on the '''Launch''' button to run autodock4.

A pop-up titled '''Autodock Process Manager''' will appear.

The process time depends on the '''parameter values''' you have set.

This will take 10 to 20 seconds.

The pop-up will automatically close when the process ends.

|-
|| Cursor on the panel.
|| Viewers please note:

If the popup appears and closes quickly within 1 or 2 seconds, an error has likely occurred.

If this happens, check your parameters and '''run '''the '''autodock''' again.
|-
|| Cursor on the home folder .

Cursor on output file '''2vta.dlg'''.

Right-click on '''2vta.dlg''' and open it using the text editor.
|| Open the''' home '''folder.

The output file '''2vta.dlg''' will be saved in the home folder.

We need to open the '''dlg '''file and check the last line to make sure '''autodock''' is successfully completed.

I will right-click and open the file using the text editor.

|-
|| Cursor on '''2vta.dlg '''document.

Scroll to the last line in the document.

Cursor on '''Autodock4 Successful Completion.'''

|| The file opened in gedit for me.

Scroll to the last line in the document.

Here you will see, '''Autodock4: Successful Completion'''.

Close the text file and close the home folder..

This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary'''
|| Let us summarize.

In this tutorial, we have,

Opened the PDBQT files for receptor and ligand for docking on ADT interface.

Performed docking using default docking parameters.

|-
|| '''Slide Number 9'''

'''Summary'''
|| Saved the output as .dpf file.

Ran AutoDock

Opened the .dlg file to make sure the autodock run is successfully completed.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| As an assignment,

Run autodock for the example 1DWD, given in the '''Examples '''folder in the Downloads page.

|-
|| '''Slide''' '''Number 11'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 113'''

'''Forum'''
||
* Please post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgement '''
||Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
|| '''Slide Number 14'''

'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}

AutoDock4/C2/Running-AutoDock/English

2024-01-17T06:40:52Z

Snehalathak:

'''Title of script''': '''Running AutoDock'''

'''Author: Dr.Snehalatha Kaliappan and Sruthi Sudhakar'''

'''Keywords: Autodock4, docking, docking parameters, genetic algorithm, dpf file, pdbqt files, dlg file, video tutorial.'''

{|border =1

|| Visual Cue
|| Narration
|-
|| '''Slide Number 1'''

'''Title Slide'''
|| Welcome to this tutorial on '''Running AutoDock'''
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to

Open the '''PDBQT''' files for receptor and ligand for docking on the '''ADT''' interface

Perform docking using default docking parameters

Save the output as '''.dpf''' file.

|-
|| '''Slide Number 3'''

'''Learning Objectives'''
|| Run AutoDock

Open the .dlg file to make sure the autodock run is successfully completed.

|-
|| '''Slide Number 4'''

'''System Requirement'''
|| Here I am using,

'''Ubuntu Linux''' OS version 20.04

AutoDockTools version 1.5.7

gedit v3.36.2
|-
|| '''Slide Number 5'''

'''Pre-requisites'''
|| To follow this tutorial you should be familiar with,

topics in basic bioinformatics

basic operations on '''AutoDock Tools''' interface
|-
|| '''Slide number 6'''

'''Code Files'''

|| The input files required for this tutorial are available in the '''Code files''' link.

Please download and extract the files.

|-
|| '''Slide number 7'''

'''Code Files'''

|| Save the input files in your home directory or working directory

Make a copy of all the files and then use them for practising

|-
|| Cursor on ADT interface.
|| Here I have opened ADT interface.

|-
|| Click on '''Docking''' on the toolbar.

Select '''Macromolecule''' from the dropdown, then click '''Set Rigid Filename.'''

Cursor on the panel.

Select '''2vta.pdbqt''' from the list of files. Click on the '''Open '''button.

|| Click on the '''Docking''' tool on the menu bar.

Select '''Macromolecule''' from the dropdown, then select '''Set Rigid Filename.'''

'''PDBQT Macromolcule File '''window opens.

Select '''2vta.pdbqt''' from the list of files and click on the '''Open '''button.

|-
|| click on '''Docking''', from the dropdown choose '''Ligand,''' select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

Cursor on the''' AutoDpf4 Ligand Parameters '''pop-up window.

Click on the '''Accept '''button in the pop-up.

|| Click on '''Docking''' again, from the dropdown choose '''Ligand,''' select '''Open''' option.

Select '''ligand.pdbqt '''from the list of files in the window.

Click on the '''Open''' button.

A pop up window '''AutoDpf4 Ligand Parameters '''appears.

Read the information about the ligand.

Some default parameters are selected, leave them as such.

Click on the '''Accept '''button in the pop-up.

The pop up window closes
|-
|| Click Docking >> Search Parameters >> Genetic Algorithm.

Cursor on '''Genetic Algorithm Parameters''' window.

Click the '''Accept''' button.

|| Click on '''Docking''' again, from the dropdown choose '''Search Parameters.'''

From the sub-menu select '''Genetic Algorithm'''.

'''Genetic Algorithm Parameters''' window opens.

You will notice that all the fields are auto populated.

We will leave the default parameters as such and click on''' Accept''' button.
|-
|| Click Docking >> Docking Parameters.

Cursor on the '''Set Docking Run Options '''window.

Click the '''Accept '''button.

|| Next click again on '''Docking''' and from the dropdown choose '''Docking Parameters'''.

'''Set Docking Run Options '''window opens.

Again you will notice that all the fields are auto populated.

We will leave them as such and click on''' Accept''' button.

|-
|| Click Docking >> Output >> Lamarckian GA(4.2).

'''Autodock4.2 GALS Docking Parameter Output File''' window opens.

Type the file name in the File name field as''' 2vta.dpf'''.

The Files of type field is auto populated as '''dpf '''file.

Click on '''Save''' Button.

|| To save all the parameters as a single docking file; click '''Docking''' again.

Choose the '''Output''' option from the dropdown.

From the sub-menu choose '''Lamarckian GA(4.2)'''.

'''Autodock4.2 GALS Docking Parameter Output File''' dialog box opens.

Type the file name in the '''File name '''field as''' 2vta.dpf'''.

The Files of type field is chosen as '''dpf''' file.

Click on '''Save''' Button.

|-
|| Click Run >> Run AutoDock.

Cursor on '''Run AutoDock''' pop-up.

|| Next, Click on '''Run''', Choose '''Run AutoDock'''.

'''Run AutoDock''' pop-up opens.

|-
|| Cursor on '''Run AutoDock''' pop-up.
|| Here you will again need to set the '''Program Pathname '''and '''Parameter Filename'''.

For me '''Program Pathname''' is already auto populated, hence I will leave it as such.

Windows users may click on the '''Browse''' button and fill the path for the '''autodock4.exe file'''.
|-
|| Click on the '''Browse''' button next to the '''Parameter Filename '''field.

From the pop-up window, choose '''2vta.dpf''' from the home folder.

|| '''Parameter Filename '''is also auto populated as '''2vta.dpf.'''

Click on the '''Browse''' button next to the field.

From the pop-up window, I will choose '''2vta.dpf''' from the home folder.

Click on the '''Open''' button in the pop-up window.

Now the empty field next to '''Log Filename''' will automatically be populated as '''2vta.dlg'''.
|-
|| Cursor on the cmd field.
|| Here you may also find the command line if you prefer to use the terminal to run '''autodock4'''.
|-
|| Click on the '''Launch''' button.

Cursor on '''Autodock process Manager''' popup.
|| Click on the '''Launch''' button to run autodock4.

A pop-up titled '''Autodock Process Manager''' will appear.

The process time depends on the '''parameter values''' you have set.

This will take 10 to 20 seconds.

The pop-up will automatically close when the process ends.

|-
|| Cursor on the panel.
|| Viewers please note:

If the popup appears and closes quickly within 1 or 2 seconds, an error has likely occurred.

If this happens, check your parameters and '''run '''the '''autodock''' again.
|-
|| Cursor on the home folder .

Cursor on output file '''2vta.dlg'''.

Right-click on '''2vta.dlg''' and open it using the text editor.
|| Open the''' home '''folder.

The output file '''2vta.dlg''' will be saved in the home folder.

We need to open the '''dlg '''file and check the last line to make sure autodock is successfully completed.

I will right-click and open the file using the text editor.

|-
|| Cursor on '''2vta.dlg '''document.

Scroll to the last line in the document.

Cursor on '''Autodock4 Successful Completion.'''

|| The file opened in gedit for me.

Scroll to the last line in the document.

Here you will see, '''Autodock4: Successful Completion.'''

Close the text file and close the home folder..

This brings us to the end of this tutorial.
|-
|| '''Slide Number 8'''

'''Summary'''
|| Let us summarize.

In this tutorial, we have,

Opened the PDBQT files for receptor and ligand for docking on ADT interface

Performed docking using default docking parameters

|-
|| '''Slide Number 9'''

'''Summary'''
|| Saved the output as .dpf file.

Ran AutoDock

Opened the .dlg file to make sure the autodock run is successfully completed.

|-
|| '''Slide Number 10'''

'''Assignment'''
|| As an assignment,

Run autodock for the example 1DWD, given in the '''Examples '''folder in the Downloads page.

|-
|| '''Slide''' '''Number 11'''

'''About Spoken Tutorial Project '''
||
* The video at the following link summarizes the Spoken Tutorial project.
* Please download and watch it.

|-
|| '''Slide Number 12'''

'''Spoken tutorial workshops '''
||
* We conduct workshops using spoken tutorials and give certificates.
* For more details, please write to us.

|-
|| '''Slide Number 113'''

'''Forum'''
||
* Please post your timed queries in this forum.

|-
|| '''Slide Number 14'''

'''Acknowledgement '''
||Spoken Tutorial project was established by the Ministry of Education (MoE), Govt. of India
|-
|| '''Slide Number 15'''

'''Acknowledgement '''
|| This tutorial is contributed by Snehalatha Kaliappan, Sruthi Sudhakar and Madhuri Ganapathi from IIT Bombay.
|-
|}