Madhurig at 09:32, 26 November 2019

2019-11-26T09:32:39Z

Madhurig at 12:50, 10 September 2018

2018-09-10T12:50:26Z

Madhurig: Created page with "{| border=1 ||'''Time''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this spoken tutorial on '''Overview of Avdogadro'''. |- || '..."

2018-09-07T06:04:41Z

Created page with "{| border=1 ||'''Time''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this spoken tutorial on '''Overview of Avdogadro'''. |- || '..."

New page

{| border=1
||'''Time'''
||'''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''' radio button.

Show the file in Downloads folder.
|| Click on '''Save File''' button.

Avogadro-1.2.On-win32.exe file downloads to the '''Downloads''' folder.

|-
|| Show the steps of installation.

Double click on '''Avogadro-1.2.On-win32.exe''' file.
|| To install '''Avogadro,''' double click on Avogadro-1.2.On-win32.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/ https://avogadro.cc]
|| Open the default web browser in '''Mac OSX'''.

In the '''address bar''' type:

[https://avogadro.cc/ 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 the left panel to open it.
|| 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/ https://avogadro.cc/docs/]

Point to the address bar.
|| Open your default web browser.

In the Address bar type:

[https://avogadro.cc/docs/ h][https://avogadro.cc/docs/ ttps://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 '''frament 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.
|-
|}

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Avogadro/C2/Overview-of-Avogadro/English - Revision history

Madhurig at 09:32, 26 November 2019

Madhurig at 12:50, 10 September 2018

Madhurig: Created page with "{| border=1 ||'''Time''' ||'''Narration''' |- || '''Slide Number 1''' '''Title Slide''' || Welcome to this spoken tutorial on '''Overview of Avdogadro'''. |- || '..."