Difference between revisions of "Avogadro/C2/Build-molecules/English"

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(Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- ||'''Slide Number 1''' '''Title Slide''' || Warm greetings everyone!! Welcome to this tutorial on '''Build Molecules'''....")
 
 
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* Show fragment library
 
* Show fragment library
  
−
* Build DNA molecules and peptides.  
+
* Build DNA molecules and '''Peptides'''.  
 
|-
 
|-
 
|| '''Slide Number 3'''
 
|| '''Slide Number 3'''
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|| Here I am using
 
|| Here I am using
  
−
* Ubuntu Linux OS version 14.04
+
* '''Ubuntu Linux''' OS version 14.04
  
−
* Avogadro version 1.1.1
+
* '''Avogadro''' version 1.1.1
  
 
* Working Internet connection.  
 
* Working Internet connection.  
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'''sourceforge.net/projects/avogadro'''.
 
'''sourceforge.net/projects/avogadro'''.
  
−
I have already downloaded Avogadro.
+
I have already downloaded '''Avogadro'''.
 
|-
 
|-
 
|| Click on''' Dash home.'''
 
|| Click on''' Dash home.'''
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|-
 
|-
 
|| Cursor on the '''Avogadro''' icon.
 
|| Cursor on the '''Avogadro''' icon.
−
|| Click on '''Avogadro''' icon to open the application window.
+
|| Click on '''Avogadro''' icon to open the application.
 
|-
 
|-
 
||  
 
||  
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Click on '''Other''' see the '''Periodic table'''.
 
Click on '''Other''' see the '''Periodic table'''.
  
−
Click on close(X).
+
Click on '''Close'''(X).
 
|| '''Element''' drop down list shows list of elements.
 
|| '''Element''' drop down list shows list of elements.
  
 
Click on '''Other''' to view the entire '''Periodic table''' in a separate window.
 
Click on '''Other''' to view the entire '''Periodic table''' in a separate window.
  
−
Click on close(X) to close the window.
+
Click on '''Close'''(X) to close the window.
 
|-
 
|-
 
|| Cursor on the Panel.
 
|| Cursor on the Panel.
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It will take a few seconds to complete the optimization.
 
It will take a few seconds to complete the optimization.
  
−
Click on '''Stop''' to close the ''' AutoOptimization Settings'''.
+
Click on '''Stop''' to close the ''' Optimization Settings'''.
 
|-
 
|-
 
|| Cursor on the Panel
 
|| Cursor on the Panel
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|| Select '''Click to Measure''' icon on the tool bar.
 
|| Select '''Click to Measure''' icon on the tool bar.
  
−
To measure distance click on any two consecutive carbon atoms.  
+
To measure distance, click on any two consecutive carbon atoms.  
  
 
To measure angles, click on any 3 consecutive atoms.
 
To measure angles, click on any 3 consecutive atoms.
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|| To save the file, click on '''File''' and '''Save As'''.
 
|| To save the file, click on '''File''' and '''Save As'''.
 
|-
 
|-
−
|| Point to the dialogue box.
+
|| Point to the dialog box.
 
|| '''Save Molecule As''' dialog box appears.
 
|| '''Save Molecule As''' dialog box appears.
 
|-
 
|-
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|-
 
|-
 
|| Point to the list of folders.
 
|| Point to the list of folders.
−
|| we can see list of folders having '''cml''' files of different chemical structures.  
+
|| We can see list of folders having '''cml''' files of different chemical structures.  
 
|-
 
|-
 
|| Double click on the folder to see '''.cml''' files.
 
|| Double click on the folder to see '''.cml''' files.
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Click on '''Insert''' button.
 
Click on '''Insert''' button.
  
−
Click on close to close the dialog box.
+
Click on '''Close''' to close the dialog box.
 
|-
 
|-
 
|| Point to the structure.
 
|| Point to the structure.
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|-
 
|-
 
|| Press '''CTRL+SHIFT+A'''.  
 
|| Press '''CTRL+SHIFT+A'''.  
−
|| The molecule is in select mode, to de-select
+
|| The molecule is in select mode.
 +
 
  
−
Press '''CTRL''', '''SHIFT''' and '''A''' keys simultaneously.
+
To de-select, press '''CTRL''', '''SHIFT''' and '''A''' keys simultaneously.
 
|-
 
|-
 
|| Show the images of '''Vitamin A''' and '''natural rubber.'''
 
|| Show the images of '''Vitamin A''' and '''natural rubber.'''
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|| Click on '''Build''' menu, navigate to '''Insert''' and select '''Fragment.'''
 
|| Click on '''Build''' menu, navigate to '''Insert''' and select '''Fragment.'''
  
−
Scroll down to '''macrocycles''' folder, double click to open.  
+
Scroll down to '''macrocycles''' folder; double click to open.  
 
|-
 
|-
 
|| Select '''porphin''' fragment.
 
|| Select '''porphin''' fragment.
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|-
 
|-
 
|| Show structure of '''chlorophyl''' molecule and '''Vitamin B12''' molecules.
 
|| Show structure of '''chlorophyl''' molecule and '''Vitamin B12''' molecules.
−
|| Using '''porphyrin''' fragment we can build complex chemical structures:
+
|| Using '''porphyrin''' fragment, we can build complex chemical structures:
  
 
Such as '''Chlorophyll''' and '''Vitamin B12'''.
 
Such as '''Chlorophyll''' and '''Vitamin B12'''.
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|| To insert a '''DNA''' molecule, go to '''Build''' menu navigate to '''Insert'''
 
|| To insert a '''DNA''' molecule, go to '''Build''' menu navigate to '''Insert'''
  
−
Select '''DNA/RNA''' from the sub-menu.
+
And click on '''DNA/RNA''' from the sub-menu.
 
|-
 
|-
 
|| Point to the box.
 
|| Point to the box.
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|-
 
|-
 
|| Point to the molecule.
 
|| Point to the molecule.
−
|| You can choose your own sequence of '''nucleic acids'''.
+
|| You can choose your own sequence of '''acids'''.
  
−
For demonstration I will select '''ATGC ATGC'''.
+
For demonstration I will select '''A T G C A T G C'''.
  
 
The order of selection of '''nucleic acids''' appear in the '''Sequence''' text box.
 
The order of selection of '''nucleic acids''' appear in the '''Sequence''' text box.
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Select '''Strands''' as '''Single''' and click on '''Insert''' button.
 
Select '''Strands''' as '''Single''' and click on '''Insert''' button.
 
|-
 
|-
−
|| Click on close(X) to close the dialog box.
+
|| Click on Close(X) to close the dialog box.
−
|| Click on close(X) to close the dialog box.
+
|| Click on '''Close'''(X) to close the dialog box.
 
|-
 
|-
 
|| Point to the molecule.
 
|| Point to the molecule.
−
|| We now have a single stranded '''DNA''' molecule on '''Panel'''.
+
|| We now have a single stranded '''DNA''' molecule on the '''Panel'''.
  
 
Zoom out the structure and drag to the centre of the '''Panel'''.
 
Zoom out the structure and drag to the centre of the '''Panel'''.
 
|-
 
|-
 
|| press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
 
|| press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
−
|| To deselect the''' DNA''' molecule on Panel,
+
|| To deselect the''' DNA''' molecule on the '''Panel''',
  
 
press '''CTRL, Shift''' and '''A''' keys simultaneously.
 
press '''CTRL, Shift''' and '''A''' keys simultaneously.
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|-
 
|-
 
|| Select '''amino acid''' sequence as Gly-Val-Pro-Cys, click on '''Insert Peptide''' button.
 
|| Select '''amino acid''' sequence as Gly-Val-Pro-Cys, click on '''Insert Peptide''' button.
−
|| Select '''amino acids''' for the '''peptide''' sequence by clicking on the '''amino acids''' buttons.  
+
|| Select '''amino acids''' for the '''Peptide''' sequence by clicking on the '''amino acids''' buttons.  
  
 
For demonstration I will choose the sequence as '''Glycine(Gly)''' -'''Valine(Val)''' -'''Proline(Pro)''' and '''Cystine(Cys)'''.
 
For demonstration I will choose the sequence as '''Glycine(Gly)''' -'''Valine(Val)''' -'''Proline(Pro)''' and '''Cystine(Cys)'''.
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|| Point to the '''Peptide '''chain.
 
|| Point to the '''Peptide '''chain.
  
−
To de-select the '''Peptide''' on '''Panel''',
+
To de-select the '''Peptide''' on '''Panel''', press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
−
 
+
−
press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
+
 
|| '''Peptide''' chain appears on the '''Panel'''.
 
|| '''Peptide''' chain appears on the '''Panel'''.
  
Line 436: Line 435:
 
* Show fragment library
 
* Show fragment library
  
−
* Build DNA molecules and peptides.
+
* Build '''DNA''' molecules and '''Peptides'''.
 
|-
 
|-
 
| | '''Slide Number 9'''
 
| | '''Slide Number 9'''
Line 456: Line 455:
 
|| Assignment:
 
|| Assignment:
  
−
* Build '''RNA''' sequence using the Nucleic acids: '''AUGC'''
+
* Build '''RNA''' sequence using the '''Nucleic acids: AUGC'''
  
 
* Optimize geometry using '''MMFF94''' force field
 
* Optimize geometry using '''MMFF94''' force field

Latest revision as of 07:45, 1 January 2016

Visual Cue Narration
Slide Number 1

Title Slide

Warm greetings everyone!!

Welcome to this tutorial on Build Molecules.

Slide Number 2

Learning Objectives

In this tutorial, we will learn to:
  • Import molecules from database
  • Rotate, zoom in and zoom out
  • Build molecules on the Panel
  • Set up force field and optimize geometry
  • Measure bond lengths, bond angles, dihedral angles
  • Show fragment library
  • Build DNA molecules and Peptides.
Slide Number 3

System Requirement

Here I am using
  • Ubuntu Linux OS version 14.04
  • Avogadro version 1.1.1
  • Working Internet connection.
Slide Number 4

Pre-requisites

To follow this tutorial you should have,
  • Knowledge of basic school Chemistry.
Slide number 5

Download Link

To download Avogadro use the link shown

sourceforge.net/projects/avogadro.

To download Avogadro please use the link shown

sourceforge.net/projects/avogadro.

I have already downloaded Avogadro.

Click on Dash home. To open Avogadro, click on Dash home.

In the search bar, type avogadro.

Cursor on the Avogadro icon. Click on Avogadro icon to open the application.
Let's begin by importing a xylene molecule from chemical structure database.
Cursor on the Panel. To import a molecule, we need a working Internet connection.
Click on File menu, navigate to Import.

Point to the sub-menu.

Click on File menu, navigate to Import.

A sub-menu opens.

Select Fetch by chemical name. Select Fetch by chemical name.
Point to Chemical name dialog box.

Type xylene in the search box, click OK button.

Chemical name dialog box appears.

For demonstration I will type xylene in the search box.

Click on OK button.

Point to xylene. We now have a xylene molecule on the Panel.
Let's rotate the molecule on the Panel.
Click on Navigation tool on the tool bar.

Hold the left mouse button and drag.

Click on Navigation tool on the tool bar.

Place the cursor on the molecule.

Hold the left mouse button and drag.

Notice the direction arrows indicating the drag.

Show the translation. To translate the molecule, use right mouse button and drag.
Scroll the mouse wheel to zoom in and zoom out. Scroll the mouse wheel to zoom in and zoom out the structure.
Cursor on the Panel. Let's learn how to create a molecule.
Click on Draw Tool icon on the tool bar. To create a molecule, click on Draw Tool icon on the tool bar.
Point to Draw Settings menu.

Point to drop downs.

Under Draw Settings menu, we can see
  • Element drop down button
  • Bond Order drop down button
  • Adjust Hydrogens check box.
uncheck adjust hydrogens check box If you don't want hydrogens on the structure, un-check Adjust Hydrogens check box.
Scroll down the list.

Click on Other see the Periodic table.

Click on Close(X).

Element drop down list shows list of elements.

Click on Other to view the entire Periodic table in a separate window.

Click on Close(X) to close the window.

Cursor on the Panel. Lets draw structure of Aniline on the Panel.
Click on Carbon.

Click on the Panel and drag.

Select Carbon from Elementdrop down list.

Select Single from Bond Order drop down.

Click on the Panel.

Drag and drop to make a closed chain of six carbon atoms.

Select Double from Bond Order.

Click on alternate positions.

To show double bonds, select Double from Bond Order drop down.

Click on alternate bonds to obtain Benzene structure.

Let's complete Aniline structure.
Select Nitrogen from Element drop down. Select Nitrogen from Element drop down list.

Select Single from Bond Order drop down.

Click on hydrogen atoms on the structure. Click on any one of the carbon atoms on the structure and drag.
Go to Build menu, select Add Hydrogens.

Point to Aniline structure.

Go to Build menu and select Add Hydrogens.


We have the structure of Aniline on the Panel.

Point to Aniline structure. To get a stable conformation, Aniline structure on the Panel needs to be optimized.
Click on Auto Optimization Tool icon on the tool bar. To optimize, click on Auto Optimization Tool on the tool bar.
Point to the menu. AutoOptimization Settings menu appears on the left.
Click on Force Field drop down list, select MMFF94. Click on Force Field drop down list, select MMFF94.

MMFF94 is generally used to optimize small organic molecules.

Click on Start button.

Click on Stop to close AutoOptimization Settings.

Click on Start button.

It will take a few seconds to complete the optimization.

Click on Stop to close the Optimization Settings.

Cursor on the Panel Let's measure bond lengths, bond angles and dihedral angles of Aniline.
Select Click to Measure icon on the tool bar.

Click on any two consecutive carbon atoms.

Click on 3 consecutive atoms.

Click on 4 successive atoms.

Point to the values.

Select Click to Measure icon on the tool bar.

To measure distance, click on any two consecutive carbon atoms.

To measure angles, click on any 3 consecutive atoms.

To measure dihedral angles, click on any 4 consecutive atoms.

Measured values appear at the bottom of the Panel.

Click on File and Save as. To save the file, click on File and Save As.
Point to the dialog box. Save Molecule As dialog box appears.
Type the File Name as Aniline.cml.

Choose file location as Desktop, click on Save button.

Type the File Name as Aniline.cml.

Choose the location as Desktop and click on Save button.

Cursor on the window. Click on New icon to open a new window.
Cursor on the Panel. Avogadro software has a feature to build complex molecules using fragment library.
Go to Build menu.

Navigate to Insert and select Fragment option.

Point to the dialog box.

Go to Build menu.

Navigate to Insert and select Fragment option.

Insert Fragment dialog box opens.

Point to the list of folders. We can see list of folders having cml files of different chemical structures.
Double click on the folder to see .cml files. For example let's open alkenes folder.

Double click on the folder to view the contents of the folder.

Select 2-methylbut-2-ene.cml.

Click on Insert button.

Click on close to close the dialog box.

Select 2-methyl-buta-1,3-diene.cml.

Click on Insert button.

Click on Close to close the dialog box.

Point to the structure. 2-methyl-1,3-butadiene structure is displayed on the Panel.

It is commonly called as Isoprene.

We can build many natural products using Isoprene.

Press CTRL+SHIFT+A. The molecule is in select mode.


To de-select, press CTRL, SHIFT and A keys simultaneously.

Show the images of Vitamin A and natural rubber.

Point to the structure.

As an example:

I will show Vitamin A and natural rubber which were built using Isoprene.

Vitamin A, natural rubber.

I will translate Isoprene to a corner.

Click on Build menu, select Fragment.

Scroll down to macrocycles,

Click on Build menu, navigate to Insert and select Fragment.

Scroll down to macrocycles folder; double click to open.

Select porphin fragment. Select porphin fragment and click on Insert.

Close the dialog box.

Show structure of chlorophyl molecule and Vitamin B12 molecules. Using porphyrin fragment, we can build complex chemical structures:

Such as Chlorophyll and Vitamin B12.

Chlorophyll

Vitamin B12.

Cursor on the Panel. Complex molecules like DNA and peptides can be easily built using Avogadro.

Open a new window using New icon.

Cursor on the menu bar.

Go to Build menu, Insert.

Select DNA/RNA from sub-menu.

To insert a DNA molecule, go to Build menu navigate to Insert

And click on DNA/RNA from the sub-menu.

Point to the box. Insert Nucleic Acids dialog box appears.
Select DNA in DNA/RNA builder. Select DNA from DNA/RNA Builder drop down.
Click on buttons. Four nucleic acid bases are shown as buttons.

Click on the buttons to choose the nucleic acid sequence.

Point to the molecule. You can choose your own sequence of acids.

For demonstration I will select A T G C A T G C.

The order of selection of nucleic acids appear in the Sequence text box.

Point to Bases Per Turn drop down, A, select "5":

Select Strands as Single, click on Insert button.

In the Bases Per Turn drop down, select A, select "5": which is the number of base pairs per Helix.

Select Strands as Single and click on Insert button.

Click on Close(X) to close the dialog box. Click on Close(X) to close the dialog box.
Point to the molecule. We now have a single stranded DNA molecule on the Panel.

Zoom out the structure and drag to the centre of the Panel.

press CTRL, Shift and A keys simultaneously. To deselect the DNA molecule on the Panel,

press CTRL, Shift and A keys simultaneously.

Click on New icon to open a new window. We can also create a Peptide sequence using Peptide option in the Insert menu.

Again click on New icon to open a new window.

Go to Build menu scroll down to, Insert, Peptide. Go to Build menu scroll down to Insert and Peptide.
Point to the box. Insert Peptide dialog box appears.
Select amino acid sequence as Gly-Val-Pro-Cys, click on Insert Peptide button. Select amino acids for the Peptide sequence by clicking on the amino acids buttons.

For demonstration I will choose the sequence as Glycine(Gly) -Valine(Val) -Proline(Pro) and Cystine(Cys).

Point to the Sequence text box.

Click on Insert Peptide button.

The order of selection appear in the Sequence text box.

Click on Insert Peptide button.

Close the Insert Peptide dialog box.

Point to the Peptide chain.

To de-select the Peptide on Panel, press CTRL, Shift and A keys simultaneously.

Peptide chain appears on the Panel.

To de-select the Peptide on Panel,

press CTRL, Shift and A keys simultaneously.

You can choose the amino acids of your choice and build the Peptide sequence.

Let's summarize.
Slide Number 8

Summary

In this tutorial we learnt to :
  • Import molecules from the database
  • Rotate, zoom in and zoom out
  • Build molecules on the panel
  • Set up force field and optimize geometry
  • Measure bond lengths, bond angles, dihedral angles
  • Show fragment library
  • Build DNA molecules and Peptides.
Slide Number 9

Assignment 1

As an assignment
  • Create a protein sequence using the following amino acid residues:

Glu, Leu, Asn, Cys, His.

  • Optimize the geometry using UFF force field
  • Save the image as .cml file.
Slide Number 10

Assignment 2

Assignment:
  • Build RNA sequence using the Nucleic acids: AUGC
  • Optimize geometry using MMFF94 force field
  • Save the image as .cml file.
Slide Number 11

Acknowledgement

Watch the video available at

http://spoken-tutorial.org/What is a Spoken Tutorial

It summarises the Spoken Tutorial project.

If you do not have good bandwidth, you can download and watch it.

  • This video summarizes the Spoken Tutorial project
  • If you do not have good bandwidth, you can download and watch it.
Slide Number 12

The Spoken Tutorial Project Team,

Conducts workshops using spoken

tutorials

Gives certificates to those who pass an online test

For more details, please write to,

contact@spoken-tutorial.org

* We conduct workshops using Spoken Tutorials and give certificates.
  • Please contact us.
Slide number 13

Spoken Tutorial Project is a part of the Talk to a Teacher project

It is supported by the National Mission on Education through ICT, MHRD, Government of India

More information on this Mission is available at:

http://spoken-tutorial.org/NMEICT-Intro

Spoken Tutorial Project is funded by NMEICT, MHRD Government of India
This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining.

Contributors and Content Editors

Madhurig, Nancyvarkey

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