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

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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13:07	This is Madhuri Ganapathi from, IIT Bombay signing off. Thank you for watching.

Contributors and Content Editors

Pratik kamble