Pratik kamble: Created page with "{| border=1 ||'''Time''' ||'''Narration''' |- |00:01 | Welcome to this spoken tutorial on '''Overview of Avdogadro'''. |- |00:05 |In this tutorial we will learn,..."

2021-06-17T07:08:49Z

Created page with "{| border=1 ||'''Time''' ||'''Narration''' |- |00:01 | Welcome to this spoken tutorial on '''Overview of Avdogadro'''. |- |00:05 |In this tutorial we will learn,..."

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{| border=1
||'''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.

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|01:03
|It is free and open source software.

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|01:06
|We can build, load and edit 3D structures of various molecules.

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|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.

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|01:40
| Click on '''Save File''' button.

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|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.

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|01:58
| Click '''Next''' button in the '''wizard''' window.

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| 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.

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|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'''.

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|02:43
|In the '''address bar''' type: [https://avogadro.cc/ 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.

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|03:03
| Select the '''Save File''' radio button.

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|03:06
| Then click on '''OK''' button at the bottom.

|-
|03:10
| '''Avogadro''' downloads as '''.dmg''' file to the '''Downloads''' folder.

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|03:16
| Double-click the folder to open it. '''Avogadro''' file browser opens.

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|03:22
| Drag the '''Avogadro''' icon to '''Applications''' folder.

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|03:26
|'''Avogadro''' software will be copied to the '''Applications''' folder.

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|03:31
| Click on '''Applications''' icon on the left panel to open it.

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|03:36
| Notice the '''Avogadro''' icon in the '''Applications''' folder. Click on '''Avogadro''' icon.

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|03:44
| '''Unidentified developer''' message appears.

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|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.

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|04:05
| In the '''unlock Security & Privacy preferences''' box, type '''username''' and '''password'''.

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|04:12
| Click '''Unlock''' button at the bottom.

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|04:15
|Under '''Allow apps downloaded from:''' select '''Anywhere''' radio button.

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|04:21
| Then click on '''Allow From Anywhere '''button.

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|04:25
| Click on '''Click the lock to make changes''' icon.

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|04:30
| Close the '''Security & Privarcy''' window.

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|04:34
| Click on '''Avogadro''' icon.

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|04:37
| A message box opens. In the box click '''Open''' button.

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|04:43
| '''Avogadro''' application opens.

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|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'''.

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|05:08
|I have already opened '''Ubuntu Software center''' using the '''Launcher'''.

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|05:13
| In the Search box type '''avogadro'''.

'''Avogadro''' icon appears.

Click on the icon.

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|05:22
| Below the icon, you can see a button named '''More Info'''. Click on this button.

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|05:29
| A window opens with all the information about '''Avogadro'''.

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|05:34
|On the right side of the window, click on '''Install''' button.

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|05:39
| Once the installation starts, '''Authenticate''' dialog-box opens.

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|05:44
| Type the '''system password''' and click on Authenticate''' button at the bottom. Installation takes a few seconds.

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|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.

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|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/ h][https://avogadro.cc/docs/ ttps://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.

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|06:46
|We will learn about each of these in detail in the series.

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|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.
|-
|}

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

Pratik kamble: Created page with "{| border=1 ||'''Time''' ||'''Narration''' |- |00:01 | Welcome to this spoken tutorial on '''Overview of Avdogadro'''. |- |00:05 |In this tutorial we will learn,..."