Difference between revisions of "Avogadro/C2/Overview-of-Avogadro/English"

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(Created page with "{| border=1 ||'''Time''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this spoken tutorial on '''Overview of Avdogadro'''. |- || '...")
 
 
(One intermediate revision by the same user not shown)
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{| border=1
 
{| border=1
−
||'''Time'''   
+
||'''Visual Cue'''   
 
||'''Narration'''   
 
||'''Narration'''   
 
|-  
 
|-  
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* About '''Avogadro '''interface  
 
* About '''Avogadro '''interface  
  
−
* Benefits of '''Avogadro '''and  
+
* Benefits of '''Avogadro''' and  
  
 
* Play video clippings of '''Avogadro''' tutorials available on our website.  
 
* Play video clippings of '''Avogadro''' tutorials available on our website.  
Line 50: Line 50:
  
 
'''About Avogadro'''  
 
'''About Avogadro'''  
−
|| Avogadro is a three dimensional Molecular builder, editor and visualization tool.  
+
|| '''Avogadro''' is a three dimensional molecular builder, editor and visualization tool.  
  
 
It is free and open source software.  
 
It is free and open source software.  
Line 56: Line 56:
 
We can build, load and edit 3D structures of various molecules.  
 
We can build, load and edit 3D structures of various molecules.  
  
−
It runs on '''Windows''', '''Mac OSX''' and '''Linux '''operating systems.  
+
It runs on '''Windows''', '''Mac OSX''' and '''Linux''' operating systems.  
  
 
|-  
 
|-  
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|| Open your default browser.  
 
|| Open your default browser.  
  
−
In the address bar type '''avogadro.cc '''and press '''Enter'''.  
+
In the address bar type '''avogadro.cc ''' and press '''Enter'''.  
  
 
|-  
 
|-  
−
|| Click on '''Download link.'''  
+
|| Click on '''Download link'''.
−
|| Click on '''Download link.'''  
+
|| Click on '''Download link'''.
  
 
|-  
 
|-  
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|-  
 
|-  
−
|| Click on '''Save File''' radio button.  
+
|| Click on '''Save File''' button.  
  
−
Show the file in Downloads folder.  
+
Show the file in '''Downloads''' folder.  
 
|| Click on '''Save File''' button.  
 
|| Click on '''Save File''' button.  
  
−
Avogadro-1.2.On-win32.exe file downloads to the '''Downloads''' folder.  
+
'''Avogadro.exe''' file downloads to the '''Downloads''' folder.  
  
 
|-  
 
|-  
 
|| Show the steps of installation.  
 
|| Show the steps of installation.  
  
−
Double click on '''Avogadro-1.2.On-win32.exe''' file.  
+
Double click on '''Avogadro.exe''' file.  
−
|| To install '''Avogadro,''' double click on Avogadro-1.2.On-win32.exe file.  
+
|| To install '''Avogadro''', double click on '''Avogadro.exe''' file.  
 
|-  
 
|-  
 
|| Point to the wizard  
 
|| Point to the wizard  
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Installation takes a few seconds.  
 
Installation takes a few seconds.  
 
|-  
 
|-  
−
|| Click on '''Finish '''button in the wizard window.  
+
|| Click on '''Finish''' button in the wizard window.  
  
 
Point to the window.  
 
Point to the window.  
−
|| Click on '''Finish '''button in the wizard window to complete the installation.  
+
|| Click on '''Finish''' button in the wizard window to complete the installation.  
  
 
'''Avogadro''' interface opens.  
 
'''Avogadro''' interface opens.  
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|-  
 
|-  
−
|| Click on '''OK '''button  
+
|| Click on '''OK''' button  
 
|| Then click on '''OK''' button at the bottom.  
 
|| Then click on '''OK''' button at the bottom.  
  
 
|-  
 
|-  
 
|| Point to '''.dmg''' file in the''' Downloads''' folder.  
 
|| Point to '''.dmg''' file in the''' Downloads''' folder.  
−
|| '''Avogadro''' downloads as '''.dmg '''file to the '''Downloads''' folder.  
+
|| '''Avogadro''' downloads as '''.dmg''' file to the '''Downloads''' folder.  
  
 
|-  
 
|-  
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|| Double-click the folder to open it.  
 
|| Double-click the folder to open it.  
  
−
'''Avogadro '''file browser opens.  
+
'''Avogadro''' file browser opens.  
  
 
|-  
 
|-  
−
|| Drag the Avogadro icon to Applications folder.  
+
|| Drag the '''Avogadro''' icon to '''Applications''' folder.  
  
 
Point to the progress bar.  
 
Point to the progress bar.  
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|-  
 
|-  
−
|| Click on '''Applications''' icon on the left panel to open it.  
+
|| Click on '''Applications''' icon on left panel to open.
 
|| Click on '''Applications''' icon on the left panel to open it.  
 
|| Click on '''Applications''' icon on the left panel to open it.  
  
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|| Open '''System Preferences '''window and select '''Security & Privacy '''option.  
 
|| Open '''System Preferences '''window and select '''Security & Privacy '''option.  
 
|-  
 
|-  
−
|| In '''Security & Privacy''' window>>  
+
|| In '''Security & Privacy''' window >>  
  
 
Select '''Click the lock to make changes''' icon.  
 
Select '''Click the lock to make changes''' icon.  
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'''Install Avogadro on Ubuntu Linux'''  
 
'''Install Avogadro on Ubuntu Linux'''  
−
|| Now, we will learn to install '''Avogadro '''on '''Ubuntu Linux '''machine.  
+
|| Now, we will learn to install '''Avogadro''' on '''Ubuntu Linux''' machine.  
  
 
|-  
 
|-  
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Show '''Ubuntu Software Center '''window  
 
Show '''Ubuntu Software Center '''window  
−
|| In '''Ubuntu Linux '''OS, we can directly download '''Avogadro''' using either-  
+
|| In '''Ubuntu Linux''' OS, we can directly download '''Avogadro''' using either-  
  
−
* '''Synaptic Package Manager '''or  
+
* '''Synaptic Package Manager''' or  
  
−
* '''Ubuntu Software center.'''  
+
* '''Ubuntu Software center'''.
  
 
|-  
 
|-  
 
|| Point to the window.  
 
|| Point to the window.  
−
|| I have already opened '''Ubuntu Software center '''using the''' Launcher.'''  
+
|| I have already opened '''Ubuntu Software center''' using the '''Launcher'''.
  
 
|-  
 
|-  
−
|| In the Search box type '''avogadro.'''  
+
|| In the Search box type '''avogadro'''.
  
 
Point to the icon.  
 
Point to the icon.  
  
 
Click on the icon.  
 
Click on the icon.  
−
|| In the Search box type '''avogadro.'''  
+
|| In the Search box type '''avogadro'''.
  
−
'''Avogadro '''icon appears.  
+
'''Avogadro''' icon appears.  
  
 
Click on the icon.  
 
Click on the icon.  
  
 
|-  
 
|-  
−
|| Point to '''More Info '''button.  
+
|| Point to '''More Info''' button.  
  
 
Click on '''More Info''' button.  
 
Click on '''More Info''' button.  
−
|| Below the icon, you can see a button named '''More Info.'''  
+
|| Below the icon, you can see a button named '''More Info'''.
  
 
Click on this button.  
 
Click on this button.  
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|| A window opens with all the information about '''Avogadro'''.  
 
|| A window opens with all the information about '''Avogadro'''.  
  
−
On the right side of the window, click on '''Install '''button.  
+
On the right side of the window, click on '''Install''' button.  
  
 
|-  
 
|-  
−
|| Point to the installation >>Point to the dialog-box.  
+
|| Point to the installation >> Point to the dialog-box.  
 
|| Once the installation starts, '''Authenticate''' dialog-box opens.  
 
|| Once the installation starts, '''Authenticate''' dialog-box opens.  
  
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'''Installation of Java Virtual Machine'''  
 
'''Installation of Java Virtual Machine'''  
−
|| Install Java Virtual Machine for smooth working of Avogadro software.  
+
|| Install '''Java Virtual Machine''' for smooth working of '''Avogadro''' software.  
  
 
Here is the link to install java.  
 
Here is the link to install java.  
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|| Open your default web browser.  
 
|| Open your default web browser.  
  
−
In the Address bar type:  
+
In the address bar type:  
 
   
 
   
 
[https://avogadro.cc/docs/ h][https://avogadro.cc/docs/ ttps://avogadro.cc/docs/]  
 
[https://avogadro.cc/docs/ h][https://avogadro.cc/docs/ ttps://avogadro.cc/docs/]  
Line 381: Line 381:
  
 
'''Benefits of Avogadro'''  
 
'''Benefits of Avogadro'''  
−
|| * It offers flexible high quality '''rendering'''  
+
||
 +
* It offers flexible high quality '''rendering'''  
  
 
* Energy minimisation can be done for the molecules to obtain stable conformations.  
 
* Energy minimisation can be done for the molecules to obtain stable conformations.  
  
−
* It has a huge '''Fragment library''' to load inbuilt '''structures '''
+
* It has a huge '''fragment library''' to load inbuilt structures  
  
−
* Files can be exported to '''png, jpg, bmp''' file formats.  
+
* Files can be exported to '''png''', '''jpg''', '''bmp''' file formats.  
  
−
* Two or more '''structures''' can be built or loaded on the panel.  
+
* Two or more structures can be built or loaded on the panel.  
  
 
|-  
 
|-  
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* Import molecules from database  
 
* Import molecules from database  
 
* Rotate, zoom in and zoom out  
 
* Rotate, zoom in and zoom out  
−
* Build molecules , show fragment library  
+
* Build molecules, show fragment library  
 
* Set up force field and optimize  
 
* Set up force field and optimize  
 
* geometry  
 
* geometry  
 
* Measure bond lengths, bond angles and dihedral angles  
 
* Measure bond lengths, bond angles and dihedral angles  
  
−
|| The first tutorial, '''Build molecules '''explains how to,  
+
|| The first tutorial, '''Build molecules''' explains how to,  
  
 
Build molecules  
 
Build molecules  
  
−
Show '''frament library'''  
+
Show '''fragment library'''  
  
−
Set up '''force''' field and optimize geometry  
+
Set up force field and optimize geometry  
  
 
Measure bond lengths, bond angles and dihedral angles.  
 
Measure bond lengths, bond angles and dihedral angles.  
Line 496: Line 497:
 
Proton transfer in molecules by changing pH values  
 
Proton transfer in molecules by changing pH values  
  
−
Load crystal structure and show Miller planes  
+
Load crystal structure and show '''Miller''' planes  
  
 
Build super cells  
 
Build super cells  
Line 510: Line 511:
 
Proton transfer in molecules by changing pH values  
 
Proton transfer in molecules by changing pH values  
  
−
Load crystal structure and show Miller planes  
+
Load crystal structure and show '''Miller''' planes  
  
 
Build super cells and nanotubes  
 
Build super cells and nanotubes  
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R-S configuration with examples  
 
R-S configuration with examples  
−
|| Next tutorial is''' Stereoisomerism.'''  
+
|| Next tutorial is''' Stereoisomerism'''.
  
  
 
This tutorial explains about,  
 
This tutorial explains about,  
  
−
'''Stereoisomerism''' with examples .
+
'''Stereoisomerism''' with examples.
  
 
|-  
 
|-  

Latest revision as of 15:02, 26 November 2019

Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this spoken tutorial on Overview of Avdogadro.
Slide Number 2

Learning Objectives

In this tutorial we will learn,
  • About Avogadro software
  • Download and installation of Avogadro
  • To open the documentation page
  • About Avogadro interface
  • Benefits of Avogadro and
  • Play video clippings of Avogadro tutorials available on our website.
Slide Number 3

System Requirement

To record this tutorial, I am using,

Ubuntu Linux OS version 14.04

Avogadro version 1.1.1

Mozilla Firefox Browser 58.0.2

A working internet connection.

Slide Number 4

Pre-requisites

To follow this tutorial you should have knowledge of high School Chemistry.
Slide Number 5

About Avogadro

Avogadro is a three dimensional molecular builder, editor and visualization tool.

It is free and open source software.

We can build, load and edit 3D structures of various molecules.

It runs on Windows, Mac OSX and Linux operating systems.

Slide Number 6

Download Avogadro on Windows OS.

Now we will download Avogadro on Windows operating system.
Type in the address bar avogadro.cc >> press Enter. Open your default browser.

In the address bar type avogadro.cc and press Enter.

Click on Download link. Click on Download link.
Point to the dialog-box. A dialog box opens, prompting us to save the file.
Click on Save File button.

Show the file in Downloads folder.

Click on Save File button.

Avogadro.exe file downloads to the Downloads folder.

Show the steps of installation.

Double click on Avogadro.exe file.

To install Avogadro, double click on Avogadro.exe file.
Point to the wizard Avogadro setup Wizard opens.
Click Next button. Click Next button in the wizard window.
Click on I Agree button. Click on I Agree button to continue installation.
Click on Create Avogadro Desktop Icon check box. Click on Create Avogadro Desktop Icon check box.
Click on Next button. Then click on Next button.
Click again on Next button. Click again on Next button.
click on Install button. Then click on Install button.

Installation takes a few seconds.

Click on Finish button in the wizard window.

Point to the window.

Click on Finish button in the wizard window to complete the installation.

Avogadro interface opens.

Slide Number 7

Install Avogadro on Mac OSX

Let's learn to install Avogadro in Mac OSX.
In the Address bar type:

https://avogadro.cc

Open the default web browser in Mac OSX.

In the address bar type:

https://avogadro.cc.

Click on Download link.

Point to the page.

Click on the Download link.

Download Avogadro from SourceForge page opens.

Point to the dialog-box. A dialog box opens prompting us to save the file.
Click on Save File radio button. Select the Save File radio button.
Click on OK button Then click on OK button at the bottom.
Point to .dmg file in the Downloads folder. Avogadro downloads as .dmg file to the Downloads folder.
Double click the folder to open it.

Point to the file.

Double-click the folder to open it.

Avogadro file browser opens.

Drag the Avogadro icon to Applications folder.

Point to the progress bar.

Drag the Avogadro icon to Applications folder.

Avogadro software will be copied to the Applications folder.

Click on Applications icon on left panel to open. Click on Applications icon on the left panel to open it.
Point to Avogadro icon in the Applications folder.

Click on Avogadro icon.

Notice the Avogadro icon in the Applications folder.

Click on Avogadro icon.

Point to the message.

Click Ok button at the bottom.

Unidentified developer message appears.

Click on the Ok button at the bottom.

Select Security & Privacy option. Open System Preferences window and select Security & Privacy option.
In Security & Privacy window >>

Select Click the lock to make changes icon.

In Security & Privacy window,

select Click the lock to make changes icon.

Point to the box.

Type the username and password.

In the unlock Security & Privacy preferences box, type username and password.
Click Unlock button at the bottom. Click Unlock button at the bottom.
Point to Allow apps downloaded from:

select Anywhere radio button.

Under Allow apps downloaded from:

select Anywhere radio button.

Cick on Allow From Anywhere button. Then click on Allow From Anywhere button.
Select Click the lock to make changes icon. Click on Click the lock to make changes icon.
Click on close(X) button. Close the Security & Privarcy window.
Click on Avogadro icon. Click on Avogadro icon.
Point to the message box.

In the box click Open button.

A message box opens.

In the box click Open button.

Point to the window. Avogadro application opens.
Cursor on Avogadro window. This means we have installed Avogadro successfully on our Mac OSX machine.
Slide Number 8

Install Avogadro on Ubuntu Linux

Now, we will learn to install Avogadro on Ubuntu Linux machine.
Show Synaptic Package Manager window

Show Ubuntu Software Center window

In Ubuntu Linux OS, we can directly download Avogadro using either-
  • Synaptic Package Manager or
  • Ubuntu Software center.
Point to the window. I have already opened Ubuntu Software center using the Launcher.
In the Search box type avogadro.

Point to the icon.

Click on the icon.

In the Search box type avogadro.

Avogadro icon appears.

Click on the icon.

Point to More Info button.

Click on More Info button.

Below the icon, you can see a button named More Info.

Click on this button.

Hover the mouse over information.

Click on Install button.

A window opens with all the information about Avogadro.

On the right side of the window, click on Install button.

Point to the installation >> Point to the dialog-box. Once the installation starts, Authenticate dialog-box opens.
Type the system password >> click on Authenticate button at the bottom.

Point to the Installation progress bar.

Type the system password and click on

Authenticate button at the bottom.

Installation takes a few seconds.

Point to the green coloured tick mark. Once the installation is complete,

you can see a green coloured tick mark on the Avogadro icon.

This means we have successfully installed Avogadro on our Ubuntu Linux machine.
Slide Number 9

Installation of Java Virtual Machine

Install Java Virtual Machine for smooth working of Avogadro software.

Here is the link to install java.

https://java.com/download.

Now I will show the documentation page of Avogadro.
type https://avogadro.cc/docs/

Point to the address bar.

Open your default web browser.

In the address bar type:

https://avogadro.cc/docs/

Point to the page. A new page open with the details about documentation of Avogadro.
Cursor on the interface. This is the Avogadro interface.
Click on each menu option and show. It has a standard menu bar with menu items.

We will learn about each of these in detail in the series.

Point to the tool bars. Below the menu bar we have various tool bars.
Now we will see the benefits of Avogadro.
Slide Number 10

Benefits of Avogadro

  • It offers flexible high quality rendering
  • Energy minimisation can be done for the molecules to obtain stable conformations.
  • It has a huge fragment library to load inbuilt structures
  • Files can be exported to png, jpg, bmp file formats.
  • Two or more structures can be built or loaded on the panel.
Slide Number 11

Video Clippings

Now, we will briefly go through the individual tutorials created in this series.
Slide Number 12

Build molecules

  • Import molecules from database
  • Rotate, zoom in and zoom out
  • Build molecules, show fragment library
  • Set up force field and optimize
  • geometry
  • Measure bond lengths, bond angles and dihedral angles
The first tutorial, Build molecules explains how to,

Build molecules

Show fragment library

Set up force field and optimize geometry

Measure bond lengths, bond angles and dihedral angles.

Play ST Here is the video clipping of this tutorial.
Slide Number 13

Edit Molecules

Add and delete atoms and bonds

Rotate bonds

Change length of the bond

Change hydrogen to methyl group

Copy, paste and join structures

The next tutorial is Edit Molecules.

This tutorial explains about, editing properties in Avogadro.

Play ST Let us listen to the video clipping of the tutorial.
Slide Number 14

Create surfaces

Properties of molecules, label the atoms with partial charge

Create Van der waals surfaces

The next tutorial in the series is Create surfaces.

This tutorial explains about,

Properties of molecules, label the atoms with partial charge

Create Van der waals surfaces.

Play ST Let us listen to the video clipping of this tutorial.
Slide Number 15

Hydrogen Bonding

How to configure Avogadro

Show Hydrogen bonding in molecules

Measure length of hydrogen bonds

Show force display type and dipole moments in molecules

Next tutorial is Hydrogen Bonding.

This tutorial explains,

How to configure Avogadro

Show hydrogen bonding in molecules

Show force display type and dipole moments in molecules.

Play ST Let us listen to the video clipping of the tutorial.
Slide Number 16

General Features in Avogadro

Proton transfer in molecules by changing pH values

Load crystal structure and show Miller planes

Build super cells

Show geometries in coordination compounds

Build nanotubes.

Next tutorial is General Features in Avogadro.


This tutorial explains about,

Proton transfer in molecules by changing pH values

Load crystal structure and show Miller planes

Build super cells and nanotubes

Show geometries in coordination compounds.

Play ST Let us listen to the video clipping of this tutorial.
Slide Number 17

Stereoisomerism

Conformational isomerism

Geometrical isomerism

R-S configuration with examples

Next tutorial is Stereoisomerism.


This tutorial explains about,

Stereoisomerism with examples.

Play ST Let us listen to the video clipping of this tutorial.
Slide Number 18

File Extensions

Prepare input files for computational chemistry programmes such as:

GAMESS, Gaussian, MOPAC, NWChem

View molecular orbitals and calculate IR spectrum using output files generated from:

GAMESS

Gaussian.

Next tutorial is File Extensions.

This tutorial explains about,

How to prepare input files for computational chemistry programmes


View molecular orbitals and calculate IR spectrum.

Play ST Let us listen to the video clipping of this tutorial.
Let us summarise now.
Slide Number 19

Summary

In this tutorial we have learnt,
  • About Avogadro software
  • Download and installation of Avogadro
  • To open the documentation page
  • About Avogadro interface
  • Benefits of Avogadro and
  • Play video clippings of Avogadro tutorials available on our website.
Slide Number 20

Assignment

As an assignment,

Install Avogadro on your machine.

Open Avogadro interface and explore.

Slide Number 21

Assignment

Another assignment.
  • Go through the menus and tool bars.
  • Change the background colour of the Panel.
Slide Number 22

About Spoken Tutorial project

The video at the following link summarises the Spoken Tutorial project.

Please download and watch it.

Slide Number 23

Spoken Tutorial workshops

The Spoken Tutorial Project team:

conducts workshops and gives certificates

For more details, please write to us.

Slide Number 24

Forum for specific 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 our team will answer them
Slide Number 25

Forum for specific questions:

The Spoken Tutorial forum is for specific questions on this tutorial
  • Please do not post unrelated and general questions on them
  • This will help reduce the clutter
  • With less clutter, we can use this discussion as instructional material.
Slide Number 26

Acknowledgement


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

Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.


More information on this mission is available at this link.

This is Madhuri Ganapathi from, IIT Bombay signing off.

Thank you for watching.

Contributors and Content Editors

Madhurig

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