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Time Narration
00:01 Welcome to this spoken tutorial on Overview of Avdogadro.
00:05 In this tutorial we will learn,

About Avogadro software

Download and installation of Avogadro

To open the documentation page

00:19 About Avogadro interface

Benefits of Avogadro and

Play video clippings of Avogadro tutorials available on our website.

00:31 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.

00:50 To follow this tutorial you should have knowledge of high School Chemistry.
00:57 Avogadro is a three dimensional molecular builder, editor and visualization tool.
01:03 It is free and open source software.
01:06 We can build, load and edit 3D structures of various molecules.
01:12 It runs on Windows, Mac OSX and Linux operating systems.
01:18 Now we will download Avogadro on Windows operating system.
01:23 Open your default browser. In the address bar type avogadro.cc and press Enter.
01:32 Click on Download link.
01:35 A dialog box opens, prompting us to save the file.
01:40 Click on Save File button.
01:43 Avogadro.exe file downloads to the Downloads folder.
01:48 To install Avogadro, double click on Avogadro.exe file. Avogadro setup Wizard opens.
01:58 Click Next button in the wizard window.
02:02 Click on I Agree button to continue installation.
02:07 Click on Create Avogadro Desktop Icon check box. Then click on Next button.
02:15 Click again on Next button.
02:18 Then click on Install button. Installation takes a few seconds.
02:25 Click on Finish button in the wizard window to complete the installation.
02:31 Avogadro interface opens. Let's learn to install Avogadro in Mac OSX.
02:39 Open the default web browser in Mac OSX.
02:43 In the address bar type: https://avogadro.cc.
02:50 Click on the Download link.
02:53 Download Avogadro from SourceForge page opens.
02:58 A dialog box opens prompting us to save the file.
03:03 Select the Save File radio button.
03:06 Then click on OK button at the bottom.
03:10 Avogadro downloads as .dmg file to the Downloads folder.
03:16 Double-click the folder to open it. Avogadro file browser opens.
03:22 Drag the Avogadro icon to Applications folder.
03:26 Avogadro software will be copied to the Applications folder.
03:31 Click on Applications icon on the left panel to open it.
03:36 Notice the Avogadro icon in the Applications folder. Click on Avogadro icon.
03:44 Unidentified developer message appears.
03:48 Click on the Ok button at the bottom.
03:52 Open System Preferences window and select Security & Privacy option.
03:59 In Security & Privacy window, select Click the lock to make changes icon.
04:05 In the unlock Security & Privacy preferences box, type username and password.
04:12 Click Unlock button at the bottom.
04:15 Under Allow apps downloaded from: select Anywhere radio button.
04:21 Then click on Allow From Anywhere button.
04:25 Click on Click the lock to make changes icon.
04:30 Close the Security & Privarcy window.
04:34 Click on Avogadro icon.
04:37 A message box opens. In the box click Open button.
04:43 Avogadro application opens.
04:46 This means we have installed Avogadro successfully on our Mac OSX machine.
04:53 Now, we will learn to install Avogadro on Ubuntu Linux machine.
04:58 In Ubuntu Linux OS, we can directly download Avogadro using either-

Synaptic Package Manager or

Ubuntu Software center.

05:08 I have already opened Ubuntu Software center using the Launcher.
05:13 In the Search box type avogadro.

Avogadro icon appears.

Click on the icon.

05:22 Below the icon, you can see a button named More Info. Click on this button.
05:29 A window opens with all the information about Avogadro.
05:34 On the right side of the window, click on Install button.
05:39 Once the installation starts, Authenticate dialog-box opens.
05:44 Type the system password and click on Authenticate button at the bottom. Installation takes a few seconds.
05:53 Once the installation is complete, you can see a green coloured tick mark on the Avogadro icon.
06:00 This means we have successfully installed Avogadro on our Ubuntu Linux machine.
06:07 Install Java Virtual Machine for smooth working of Avogadro software.
06:13 Here is the link to install java. https://java.com/download.
06:16 Now I will show the documentation page of Avogadro.
06:21 Open your default web browser.
06:24 In the address bar type:


06:32 A new page open with the details about documentation of Avogadro.
06:39 This is the Avogadro interface.
06:42 It has a standard menu bar with menu items.
06:46 We will learn about each of these in detail in the series.
06:52 Below the menu bar we have various tool bars.
06:57 Now we will see the benefits of Avogadro.
07:01 It offers flexible high quality rendering

Energy minimisation can be done for the molecules to obtain stable conformations.

07:12 It has a huge fragment library to load inbuilt structures

Files can be exported to png, jpg, bmp file formats.

07:24 Two or more structures can be built or loaded on the panel.
07:29 Now, we will briefly go through the individual tutorials created in this series.
07:35 The first tutorial, Build molecules explains how to,

Build molecules

Show fragment library

07:44 Set up force field and optimize geometry

Measure bond lengths, bond angles and dihedral angles.

07:53 Here is the video clipping of this tutorial.
08:08 The next tutorial is Edit Molecules. This tutorial explains about, editing properties in Avogadro.
08:18 Let us listen to the video clipping of the tutorial.
08:33 The next tutorial in the series is Create surfaces.
08:37 This tutorial explains about, Properties of molecules, label the atoms with partial charge
08:44 Create Van der waals surfaces.
08:47 Let us listen to the video clipping of this tutorial.
09:05 Next tutorial is Hydrogen Bonding.
09:08 This tutorial explains, How to configure Avogadro
09:12 Show hydrogen bonding in molecules
09:18 Show force display type and dipole moments in molecules.
09:23 Let us listen to the video clipping of the tutorial.
09:37 Next tutorial is General Features in Avogadro.
09:42 This tutorial explains about, Proton transfer in molecules by changing pH values
09:50 Load crystal structure and show Miller planes Build super cells and nanotubes
09:57 Show geometries in coordination compounds.
10:01 Let us listen to the video clipping of this tutorial.
10:20 Next tutorial is Stereoisomerism. This tutorial explains about, Stereoisomerism with examples.
10:30 Let us listen to the video clipping of this tutorial.
10:48 Next tutorial is File Extensions.
10:52 This tutorial explains about, How to prepare input files for computational chemistry programmes
11:00 View molecular orbitals and calculate IR spectrum.
11:04 Let us listen to the video clipping of this tutorial.
11:20 Let us summarise now.
11:22 In this tutorial we have learnt,

About Avogadro software

Download and installation of Avogadro

11:32 To open the documentation page

About Avogadro interface

Benefits of Avogadro and

11:40 Play video clippings of Avogadro tutorials available on our website.
11:47 As an assignment,

Install Avogadro on your machine.

Open Avogadro interface and explore.

11:55 Another assignment.

Go through the menus and tool bars.

Change the background colour of the Panel.

12:04 The video at the following link summarises the Spoken Tutorial project. Please download and watch it.
12:12 The Spoken Tutorial Project team: conducts workshops and gives certificates
12:18 For more details, please write to us.
12:21 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

12:38 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.

12:56 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this mission is available at this link.
13:07 This is Madhuri Ganapathi from, IIT Bombay signing off. Thank you for watching.

Contributors and Content Editors

Pratik kamble