Avogadro/C2/Overview-of-Avogadro/English-timed

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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:

https://avogadro.cc/docs/

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.

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12:21 Do you have questions in THIS Spoken Tutorial?

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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