Difference between revisions of "Jmol-Application/C2/Overview-of-Jmol-Application/English"

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{| style="border-spacing:0;"
 
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! <center>Visual Cue</center>
 
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! <center>Narration</center>
 
  
 +
 +
{|border=1
 +
||'''Visual Cue'''
 +
||'''Narration'''
 +
|-
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 1'''
+
|| '''Slide Number 1'''
  
 
'''Title Slide'''
 
'''Title Slide'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Welcome to this Overview tutorial on Jmol Application series.
+
|| Welcome to this tutorial on '''Overview of''' '''Jmol Application'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 2'''
+
|| '''Slide Number 2'''
  
 
'''Learning Objectives'''
 
'''Learning Objectives'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial we will go through,  
+
|| In this tutorial we will learn,  
  
 +
* About '''Jmol Application'''.
 +
* Download and run '''Jmol Application''' on '''Linux Operating System'''.
 +
* Uses and advantages.
 +
* Play video clippings of '''Jmol Application''' tutorials available on our website.
  
−
Important features of Jmol Application.
+
|-
 +
|| '''Slide Number 3'''
  
 +
'''System Requirement'''
 +
|| To record this tutorial, I am using,
  
−
Information regarding download and installation on various operating systems.
 
  
 +
* '''Ubuntu Linux''' OS version 14.04
 +
* '''Java '''(JVM) version 1. 8
 +
* '''Firefox web browser''' 54.0, and
 +
* A working''' internet''' connection
  
−
Uses of Jmol Application.
+
|-
 +
|| '''Slide Number 4'''
  
 +
'''Pre-requisites'''
 +
|| To follow this tutorial you should have knowledge of high school chemistry.
 +
 +
|-
 +
|| '''Slide Number 5'''
 +
 +
'''About Jmol Application'''
 +
 +
 +
|| About '''Jmol Application'''.
 +
 +
'''Jmol''' is an open source '''3D viewer''' for:
 +
 +
* Chemical structures.
 +
* Biomolecules
 +
* Crystal structures and
 +
* Materials.
  
−
We will Play clippings of video tutorials available in Jmol Application series at our website.
+
It runs on '''Windows, Mac, Linux''' operating systems and '''Android''' devices.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 3'''
+
|| '''Slide Number 6'''
  
−
'''Pre-requisites'''
+
'''About Jmol Application'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should have knowledge of,
+
  
  
−
High School chemistry
+
|| It can be used to create and edit models of chemical structures.
  
  
−
Or Basic Organic Chemistry
+
'''Jmol''' is used by students, educators, and researchers in the fields of '''chemistry''' and '''biochemistry'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 4'''
+
|| '''Slide Number 7'''
 +
 
 +
'''Official Jmol Website'''
  
−
'''System Requirement'''
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial, I am using,
 
  
−
'''Ubuntu '''OS version 12.10
 
  
−
'''Jmol v'''ersion 14.1.11
+
|| Here is the official website address for '''Jmol Application'''.
  
−
'''Java''' version 7
 
  
−
and Mozilla Firefox Browser 35.0
+
'''http://jmol.sourceforge.net'''
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 5'''
+
|| Open Firefox browser and type
  
−
'''What is Jmol Application?'''
+
[http://jmol.sourceforge.net/ http://jmol.sourceforge.net]
  
 +
Press Enter.
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About Jmol Application,
 
  
−
Jmol is a molecular viewer for three-dimensional chemical structures and macromolecules.
+
Point to webpage.
 +
|| Open this link in any '''web browser'''.
 +
A web-page opens.
  
  
−
Jmol can be used to create and edit 3D models of chemical structures.
+
|-
 +
|| Point to the links.
 +
|| At the top-right corner of the page we see links for
  
 +
* '''Demonstration pages''',
 +
* '''Documentation''',
 +
* '''Wiki''',
 +
* '''Download''' and others
  
−
This software can be used by students, educators, and researchers in chemistry and biochemistry.
+
|-
 +
|| Click on “'''Download'''” link provided at the top right corner of the page.
 +
|| To download '''Jmol Application''', click on the '''Download''' link.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 6'''
+
|| Point towards headings.
  
−
'''Important Features'''
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here are some important features of Jmol.
 
  
 +
Scroll down to show each heading.
 +
|| The '''Download''' page opens with headings:
  
−
It is a Free and Open Source Software.
+
Scroll down to see the details.
  
 +
* '''Downloading Jmol,'''
 +
* '''Requirements'''
 +
* '''Installing and running Jmol '''
 +
* '''Subversion Access'''
  
−
Works on Windows, Mac Operating System, Linux and also on android devices.
+
|-
 +
|| Scroll down to requirements page.
  
 +
Point to the line standalone '''Jmol Application''' requires '''Java''' 1.4 or higher.
 +
|| Scroll up to the '''Requirements''' section.
  
−
It supports all major web browsers.
+
Please note - standalone '''Jmol Application''' requires '''Java''' 1.4 or higher.  
  
 +
|-
 +
|| High-light the sentence on the page.
 +
|| If you do not have '''Java''' installed on your system, click on the '''link''' provided here.
 +
Follow the instructions.
  
−
No special hardware is required for high quality 3D-rendering.
+
|-
 +
|| Scroll down, high-light the sentence.
 +
|| Also read instructions for '''Installing and Running Jmol.'''
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 7'''
+
|| Scroll up, under heading '''Downloading Jmol, '''
  
−
'''Important Features'''
 
  
 +
Click on '''Download link.'''
 +
|| Scroll up the page.
 +
Under the heading '''Downloading Jmol, '''click on '''download link.'''
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Images can be exported to various file formats: Such as
+
|-
 +
|| Point to the prompt.
 +
|| A new page opens.
  
−
jpg, png, gif, pdf etc.
+
A '''prompt''' appears that says download will start in a few seconds.
  
 +
|-
 +
|| A dialog box appears, click on''' save file '''option.
  
−
Reads various file formats such as pdb, cif, mol, cml, xyz etc
+
Click on '''OK''' button.
 +
|| After this, a dialog box appears which prompts you to save the file.
  
 +
Click on '''Save file '''option.
  
−
If you are connected to internet you can directly
+
Then click on '''OK''' button.
  
−
loads models on Jmol panel:
+
|-
 +
||
 +
|| Depending on the '''Internet''' speed, It may take a few minutes to complete the download.
  
 +
|-
 +
|| Open the downloads directory.
  
−
From databases such as pubchem for chemical structures.
 
  
 +
|| '''Jmol binary.zip file '''gets downloaded to the''' Downloads '''directory.
  
−
And PDB database for proteins and macromolecules.
 
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 8'''
+
|| Point to the file in the directory.
 +
|| Go to the directory where you have downloaded the file.
  
−
'''Important Links'''
+
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| More information about this software is available at the following links.  
+
|| Right-click and click on Extract Here.
  
  
−
http://jmol.sourceforge.net/
+
|| Then extract the contents of the folder.
  
−
[http://www.jmol.org/ http://www.jmol.org/]
 
  
 +
Right-click on the '''zip''' file, from the context menu select '''Extract Here'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 9'''
+
|| Double-Click on open the folder.
 +
Scroll down.
  
−
'''Uses of Jmol'''
+
|| Double-click on the extracted folder to open it.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Uses of Jmol.
+
  
−
Jmol can be used:
+
Scroll down and find Jmol.jar file.
  
−
as a teaching tool to explain concepts in chemistry.
+
|-
 +
|| Cursor on Jmol.jar file.
 +
|| For windows and Mac double-click on Jmol.jar file to open the Jmol interface.
  
 +
|-
 +
|| Cursor on the window.
 +
|| I am using '''Ubuntu Linux''' operating system.
  
−
And for producing high quality 3D images that can be used in print media:
 
  
 +
I will show how to run '''Jmol Application''' on my system.
  
−
such as journals, publications and books.
+
|-
 +
|| Right-click on '''Jmol.jar''' file.  
  
  
−
And also for presentations in classrooms and lectures.
+
From the options in the context menu, I will select '''Open with Oracle Java 8 Runtime'''.
  
−
|-
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 10'''
 
  
−
'''Uses of Jmol'''
+
Cursor on Jmol window.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Jmol can also be used for molecular modelling.
+
|| Right-click on '''Jmol.jar''' file. A '''context menu''' opens with options.
  
−
And producing animation movies.
+
 
 +
I have already installed '''Java 8 Runtime Environment''' on my system.
 +
 
 +
 
 +
Fom the options in the context menu, I will select '''Open with Oracle Java 8 Runtime'''.
 +
 
 +
 
 +
'''Jmol Application''' interface opens.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the below link
+
||
 +
|| Another method to open '''Jmol''' interface is through '''terminal'''.
 +
 
 +
|-
 +
|| Press Ctrl, Alt and T keys simultaneously.
 +
|| Open the '''terminal''' by pressing '''Ctrl, Alt''' and '''T''' keys simultaneously.
 +
 
 +
|-
 +
|| At the prompt type, cd Downloads, press enter.
 +
 
 +
Then type, jmol-14.29.42
 +
 
 +
Press enter.
 +
 
 +
|| Navigate to '''Jmol''' folder which we had downloaded and extracted earlier.
 +
 
 +
 
 +
To do so, at the '''prompt''' type '''cd space Downloads''', press '''Enter'''.
 +
 
 +
 
 +
Then type '''cd''' space and the name of the '''Jmol''' folder. In my case, it is '''Jmol hyphen fourteen dot twenty-nine dot four two'''
 +
 
  
−
[http://www.umass.edu/molvis/bme3d/ http://www.umass.edu/molvis/bme3d/]
+
You may have a different name depending on the version you have downloaded.
  
−
materials/jtat_080510/_docs/slides.htm
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is the webpage that describes how to incorporate Jmol images in powerpoint presentations.
 
  
 +
Press '''Enter'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 11'''
+
|| Then type, java -jar Jmol.jar. Press enter.
 +
|| Then type '''java space hyphen jar space Jmol.jar'''
  
−
'''Teaching Chemistry using Jmol.'''
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Jmol can be effectively used to teach certain topics in chemistry which require 3D visualization.
 
  
 +
Press '''Enter'''.
  
−
At Basic level, topics such as:
 
  
 +
'''Jmol Application''' interface opens.
  
−
Structure and functional groups.
+
|-
 +
|| '''Slide number 8'''
 +
 
 +
'''Installation on Linux OS'''
 +
 
 +
 
 +
'''https://spoken-tutorial.org'''
 +
|| Linux users can also install '''Jmol''' using '''Ubuntu Software Center '''or''' Synaptic Package Manager.'''
  
  
−
Atomic and Molecular orbitals.
+
For information on how to use these, please see the '''Linux''' series on this website.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 12'''
+
|| Point to Jmol menu bar and toolbar.
  
−
'''Teaching Chemistry using Jmol.'''
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| At advanced levels Jmol can be used to teach topics such as
 
  
  
−
Stereochemistry which involves the study of spatial arrangement of atoms in a molecule.
+
|| Back to '''Jmol''' interface.
  
  
−
Symmetry and point-groups.
+
Many features of '''Jmol''' are available in the menus on the menu bar and the toolbar.  
  
 +
|-
 +
|| Click on Help Menu.
  
−
Crystal Structure and Unit cell.
 
  
 +
Click on '''Jmol Wiki'''.
  
−
And Predict proton NMR spectrum for molecules.
 
  
 +
Close the page.
 +
|| Click on '''Help''' menu.
  
−
This feature available in Jmol version 14.0 and above.
 
  
 +
Here we have link for''' Jmol Wiki '''main page.
  
−
Jmol can be used to study Structure Activity Relationships.
+
 
 +
Click on '''Jmol Wiki'''.
 +
 
 +
 
 +
If you are connected to the internet '''Jmol Wiki '''main page opens in the '''web browser'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 13'''
+
|| Cursor on the page.
 +
|| This page has detailed information about '''Jmol''' and '''Jsmol'''.
  
−
'''Download and Installation'''
 
  
 +
'''JSmol''' is a '''Java''' independent version of '''Jmol.'''
  
 +
It runs in any '''HTML5 web browser'''.
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Lets see how to download and install Jmol.
+
|-
 +
|| Point to the links.
  
  
−
Jmol can be installed on Windows, Mac operating system and on Linux systems.
+
Point to all the sections.
 +
|| This page has links to various pages on the left panel.
  
  
−
A special version of Jmol for Android devices is available at the link shown below.  
+
The page also has various sections for topics such as
 +
 
 +
* '''About Jmol and JSmol''',
 +
* '''Installation''',
 +
* '''Development''' etc.
 +
 
 +
|-
 +
|| Cursor on '''Jmol/JSmol Community''' section.
 +
 
 +
Click on '''Community and Users''' link.
 +
|| The section for '''Jmol Community''' has links to
  
 +
'''Community and Users''' and '''Communities'''.
  
−
http://wiki.jmol.org/index.php/Support/Android
 
  
 +
Click on '''Community and Users''' link.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 14'''
+
|| Cursor on '''Community '''page.
  
−
'''Download and Installation on Linux OS'''
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For Linux operating systems, download using Ubuntu software center or Synaptic package manager.
 
  
 +
|| '''Community''' page opens.
  
−
Follow this tutorial in the linux series on our website.
+
On this page you will find the work description of group of '''Jmol''' developers and '''Jmol''' users.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 15'''
+
|| Cursor on '''sub-communities'''.
  
−
'''Download and Installation'''
+
I will click on '''Crystal community'''.
  
−
'''for '''
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For Windows and Mac operating systems:
 
  
−
Open the given link in any web browser.
+
|| Different web pages for various '''sub-communities''' are available here.
  
 +
I will click on '''Crystal community'''.
  
−
[http://www.jmol.sourceforge.net/ www.][http://www.jmol.sourceforge.net/ jmol.][http://www.jmol.sourceforge.net/ sourceforge.net]
 
  
 +
Here '''Jmol''' users can discuss their experiences in using '''Jmol''' for displaying crystal structures.
  
−
I will open this link and quickly go through the contents given on the web-page.
+
Please explore these pages according to your interest.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on web-page.
+
|| '''Slide number 9'''
  
 +
'''Advantages of Jmol Application'''
  
−
Scroll down the page.
+
|| Advantages of '''Jmol Application.'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This web-page gives a lot of general information about Jmol.
+
  
−
Scroll down the page.
+
* No special hardware is required for high quality 3D-rendering.
  
 +
* If you are connected to internet you can directly
  
−
It gives information about the overview, demonstration pages, features.
+
load models on '''Jmol '''panel from '''PubChem''' and '''PDB databases'''.
  
 +
|-
 +
|| '''Slide Number 10'''
  
−
To download Jmol click on the downloads page.
+
'''Uses of Jmol'''
 +
|| '''Jmol''' can be effectively used to teach certain topics in Chemistry.
  
 +
For example:
  
−
Follow the instructions given on the page to download.
+
* Structure and functional groups.
 +
* Atomic and Molecular orbitals.
 +
* Stereochemistry
 +
* Symmetry and point-groups.
 +
* Crystal structure and Unit cell.
  
 +
|-
 +
|| '''Slide Number 11'''
  
−
Information about installing and running Jmol is also given on this page.
+
'''Uses of Jmol Application'''
 +
||
  
 +
* High quality 3D images can be produced,
 +
 +
they can be used in publications and presentations
 +
 +
* View simulated '''proton and carbon 13 NMR spectra '''for molecules.
 +
 +
* This feature is available in '''Jmol '''version 14.0 and above.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 16'''
+
|| '''Slide Number 12'''
  
−
'''Video Clippings'''
+
'''Uses of Jmol Application'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I have created a series of tutorials which describe how to use this software.
+
|| '''Jmol''' can also be used to study
  
 +
* Structure Activity Relationships
 +
* Molecular modelling
 +
* Animation of molecules
  
  
 +
|-
 +
|| '''Slide Number 13'''
 +
 +
'''Video Clippings'''
 +
|| We have created a series of tutorials which describe how to use this software.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on menu bar and tool bar.
+
|| '''Slide Number 14'''
  
 +
'''Introduction to Jmol Application'''
  
−
Click on the modelkit menu.
 
  
 +
Show the tutorial clipping of '''Introduction to Jmol Application''' tutorial.
 +
|| The first tutorial is '''Introduction to Jmol Application''',
  
−
Show the tutorial clipping of “Introduction to Jmol Application” tutorial.
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The first tutorial “Introduction to Jmol Application” has information regarding the various features available on Jmol window.
 
  
 +
It explains various features available on '''Jmol '''window.
  
−
Here is the video clipping of that video.
+
 
 +
* Create models of simple organic molecules.
 +
* Energy minimization and
 +
* Save image.
 +
 
 +
Here is the video clipping.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Show the tutorial clipping of “Create and Edit” tutorial.
+
|| '''Slide Number 15 '''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To create and edit molecular models, follow the tutorial “Create and Edit”.
+
  
 +
'''Create and Edit Molecular Models'''
  
−
Here is the clipping.
+
Show the tutorial clipping of “Create and Edit” tutorial.
 +
|| Next tutorial '''Create and Edit Molecular Models''' explains how to
  
 +
 +
* Add functional group
 +
* Add and delete bonds
 +
* Add and delete atoms
 +
* Pop-up-menu.
 +
 +
Here is the video clipping.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Show the tutorial clipping of “Measurements and labeling”
+
|| Slide Number 16
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can Measure bond lengths, bond angles and dihedral angles.
+
  
 +
'''Modify Display and View'''
 +
 +
 +
Show the tutorial clipping of '''Modify Display and View''' tutorial.
 +
|| Next tutorial '''Modify Display and View '''explains,
 +
 +
* How to, modify the view.
 +
* Change the style of the display.
 +
* Save the image in various file formats.
  
 
Here is the video clipping.
 
Here is the video clipping.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Show the tutorial clipping of “Surface and orbitals”
+
|| '''Slide Number 17'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Using Jmol we can show surfaces and create atomic and molecular orbitals.
+
  
 +
'''Measurements and Labeling'''
 +
 +
 +
Show the tutorial clipping of '''Measurements and labeling'''
 +
|| '''Next tutorial Measurements and Labeling''' tutorial explains,
 +
 +
 +
* How to measure bond lengths, bond angles and dihedral angles for a model.
 +
* Label atoms with symbols and number.
  
 
Here is the video clipping.
 
Here is the video clipping.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Show the tutorial clipping of “Plane of symmetry and point-groups”
+
|| '''Slide Number 18'''
 +
 
 +
'''Script Console and Script Commands'''
  
  
 +
Show the tutorial clipping of '''Script console and Script commands'''
 +
|| Next tutorial '''Script Console and Script Commands''' explains
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This video explains how to show Plane of symmetry and point-groups.
 
  
 +
* How to use script console and write script commands.
  
 
Here is the video clipping.
 
Here is the video clipping.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Show the tutorial clipping of''' '''“Crystal structure and Unit Cell”
+
|| '''Slide Number 19'''
  
 +
'''Surfaces and Orbitals'''
  
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Crystal structures and unit cell can be viewed using Jmol.Here is the video clipping.
+
Show the tutorial clipping of '''Surface and orbitals'''.
 +
|| Next tutorial '''Surfaces and Orbitals '''demonstrates how to-
  
−
|-
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Show the tutorial clipping of “Proteins and macromolecules”
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is the video clipping to show proteins and macromolecules in Jmol.
 
  
−
|-
+
* show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 17'''
+
  
−
'''Simulated H NMR'''
+
Here is the video clipping.
  
 +
|-
 +
|| '''Slide number 20'''
  
 +
'''Structures from Database'''
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A simulated H NMR spectrum can be displayed for all the molecules listed in chemical structure database:
 
  
 +
Show the tutorial clipping of “Structures from Database”
 +
|| Next tutorial '''Structures from Database '''explains-
  
−
Starting from Jmol version 14.0
 
  
 +
* How to load structures directly from chemical structure database such as '''PubChem'''.
 +
* Convert 2D structures drawn in GChemPaint to 3D models in Jmol
  
−
Let me open Jmol window and demonstrate this feature.
+
Here is the video clipping.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel
+
|| '''Slide number 21'''
  
 +
'''Crystal structure and Unit Cell'''
  
−
Go to tools menu, scroll down to “spectra”, then click on “proton spectra”.
 
  
 +
Show the tutorial clipping of''' '''
  
−
Scroll down the file menu, click on “add simulation”.
+
'''Crystal structure and Unit Cell'''
 +
|| Next tutorial '''Crystal structure and Unit Cell '''shows demonstration of-
  
  
−
In the dialog box, type “nitrobenzene”.
+
* Download and open '''CIF''' files in Jmol.
 +
* Display '''unit cell''' and '''unit cell''' parameters.
 +
* Display crystal structures of different crystal systems.
  
 +
Here is the video clipping.
 +
|-
 +
|| '''Slide number 22'''
  
−
Click on ok button.
+
'''Proteins and macromolecules'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To view simulated proton NMR:
+
  
−
Go to tools menu.
+
Show the tutorial clipping of '''Proteins and macromolecules''' and “3D models of Enzymes”
 +
|| Next tutorial,''' Proteins and macromolecules '''tutorial demonstrates how to  
  
−
Scroll down to “spectra” and click on “spectrum”.
 
  
 +
* Download '''pdb''' files from database.
 +
* View and modify secondary structure of a protein.
  
−
The Jspecview window opens.  
+
Here is the video clipping of this tutorial.  
  
 +
|-
 +
|| '''Slide number 23'''
  
−
Scroll down the file menu, click on “add simulation”
+
'''3D Models of Enzymes'''
  
  
−
In the dialog box enter the name of the molecule.
+
Show the tutorial clipping of “Plane of symmetry and point-groups”
 +
|| Next tutorial '''3D Models of Enzymes''' explains how to-
  
  
−
Let us type “nitrobenzene”, click on ok button.  
+
* Modify the display of secondary structure.
 +
* Highlight amino acid residues and substrate.
 +
* View Ramachandran plot for proteins.
  
 +
Here is the video clipping of this tutorial.
  
−
A proton NMR spectrum of nitrobenzene is displayed on the panel.
+
|-
 +
|| '''Slide number 24'''
 +
 
 +
'''Symmetry and Point Groups'''
 +
 
 +
Show the tutorial clipping of '''Symmetry and Point Groups'''
 +
|| Next tutorial '''Symmetry and Point Groups '''demonstrates
  
 +
* C2 and C3 rotational axes, reflection planes and point group classification.
  
−
Atoms on the structure are correlated with signals in the spectrum.
+
Here is the video clipping
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 18'''
+
|| '''Slide number 25'''
  
−
'''Animating Vibrations'''
+
'''Animation using Script Commands'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Certain files include information about molecular vibrations, such as GAMESS .log files and Spartan output files.
+
  
  
−
We can open these files in Jmol and view vibrations.
+
Show the tutorial clipping of '''Animation using Script Commands '''
 +
|| Next tutorial '''Animation using Script Commands''' demonstrates
  
−
|-
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the file CO2-DZV-hess.log
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let me open a log file showing vibrations in carbondioxide molecule.
 
  
−
|-
+
* Animation using '''script commands'''.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the file''' '''C6H6.smol
+
* Save the animation as '''GIF''' file.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is an animation, showing vibrations in benzene molecule.
+
  
−
|-
+
Here is the video clipping
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open the file cyclohexane_movie.xyz
+
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is the animation showing conformations in cyclohexane molecule.
+
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 19'''
+
|| '''Slide Number 26'''
  
 
Summary
 
Summary
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let us summarize,
+
|| Let us summarize,
  
−
In this tutorial we have learnt,
+
In this tutorial we have learnt,  
  
−
Important features of Jmol Application.
+
* About Jmol Application.
 +
* Download and run Jmol Application on Linux OS.
 +
* Uses and advantages.
 +
* Play video clippings of Jmol Application tutorials available on our website.
  
−
Information regarding Installation on various operating systems.
+
|-
 +
|| '''Slide Number 27'''
  
−
Uses of Jmol Application.
+
'''Assignment'''
 +
|| As an assignment-
 +
 
 +
1. Explore Jmol Application interface.
 +
 
 +
2. On the '''Jmol Wiki''' main page, explore '''Jmol Documentation''' page.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 20'''
+
|| '''Slide Number 28'''
  
−
'''Summary'''
+
'''About Spoken Tutorial project'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We have also seen clippings of video tutorials in Jmol Application series.
+
|| The video at the following link summarizes the Spoken Tutorial project.
  
−
And some animation videos showing vibrations and conformations of cyclohexane.
+
Please download and watch it.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 21'''
+
|| '''Slide Number 29'''
  
−
'''Acknowledgement '''
+
'''Spoken Tutorial workshops'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The video at the following link summarizes the Spoken Tutorial project.
+
|| The '''Spoken Tutorial Project '''team:
  
−
Please download and watch it.  
+
* conducts workshops using spoken tutorials and</nowiki>
 +
 
 +
* gives certificates on passing online tests.</nowiki>
 +
 
 +
For more details, please write to us.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide Number 22'''
+
|| '''Slide Number 30'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.
+
  
−
For more details, please write to us.  
+
'''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.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 23'''
+
|| '''Slide Number 31'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.  
+
 
 +
'''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 32'''
 +
 
 +
'''Acknowledgemen'''t
 +
|| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
 +
 
 +
More information on this mission is available at
  
−
More information on this Mission is available at the link shown.  
+
this link.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| '''Slide number 23'''
+
|| '''Slide number 32'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
|| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
  
 
|}
 
|}

Revision as of 15:20, 15 May 2019


Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Overview of Jmol Application.
Slide Number 2

Learning Objectives

In this tutorial we will learn,
  • About Jmol Application.
  • Download and run Jmol Application on Linux Operating System.
  • Uses and advantages.
  • Play video clippings of Jmol Application tutorials available on our website.
Slide Number 3

System Requirement

To record this tutorial, I am using,


  • Ubuntu Linux OS version 14.04
  • Java (JVM) version 1. 8
  • Firefox web browser 54.0, and
  • 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 Jmol Application


About Jmol Application.

Jmol is an open source 3D viewer for:

  • Chemical structures.
  • Biomolecules
  • Crystal structures and
  • Materials.

It runs on Windows, Mac, Linux operating systems and Android devices.

Slide Number 6

About Jmol Application


It can be used to create and edit models of chemical structures.


Jmol is used by students, educators, and researchers in the fields of chemistry and biochemistry.

Slide Number 7

Official Jmol Website


Here is the official website address for Jmol Application.


http://jmol.sourceforge.net

Open Firefox browser and type

http://jmol.sourceforge.net

Press Enter.


Point to webpage.

Open this link in any web browser.

A web-page opens.


Point to the links. At the top-right corner of the page we see links for
  • Demonstration pages,
  • Documentation,
  • Wiki,
  • Download and others
Click on “Download” link provided at the top right corner of the page. To download Jmol Application, click on the Download link.
Point towards headings.


Scroll down to show each heading.

The Download page opens with headings:

Scroll down to see the details.

  • Downloading Jmol,
  • Requirements
  • Installing and running Jmol
  • Subversion Access
Scroll down to requirements page.

Point to the line standalone Jmol Application requires Java 1.4 or higher.

Scroll up to the Requirements section.

Please note - standalone Jmol Application requires Java 1.4 or higher.

High-light the sentence on the page. If you do not have Java installed on your system, click on the link provided here.

Follow the instructions.

Scroll down, high-light the sentence. Also read instructions for Installing and Running Jmol.
Scroll up, under heading Downloading Jmol,


Click on Download link.

Scroll up the page.

Under the heading Downloading Jmol, click on download link.

Point to the prompt. A new page opens.

A prompt appears that says download will start in a few seconds.

A dialog box appears, click on save file option.

Click on OK button.

After this, a dialog box appears which prompts you to save the file.

Click on Save file option.

Then click on OK button.

Depending on the Internet speed, It may take a few minutes to complete the download.
Open the downloads directory.


Jmol binary.zip file gets downloaded to the Downloads directory.


Point to the file in the directory. Go to the directory where you have downloaded the file.
Right-click and click on Extract Here.


Then extract the contents of the folder.


Right-click on the zip file, from the context menu select Extract Here.

Double-Click on open the folder.

Scroll down.

Double-click on the extracted folder to open it.

Scroll down and find Jmol.jar file.

Cursor on Jmol.jar file. For windows and Mac double-click on Jmol.jar file to open the Jmol interface.
Cursor on the window. I am using Ubuntu Linux operating system.


I will show how to run Jmol Application on my system.

Right-click on Jmol.jar file.


From the options in the context menu, I will select Open with Oracle Java 8 Runtime.


Cursor on Jmol window.

Right-click on Jmol.jar file. A context menu opens with options.


I have already installed Java 8 Runtime Environment on my system.


Fom the options in the context menu, I will select Open with Oracle Java 8 Runtime.


Jmol Application interface opens.

Another method to open Jmol interface is through terminal.
Press Ctrl, Alt and T keys simultaneously. Open the terminal by pressing Ctrl, Alt and T keys simultaneously.
At the prompt type, cd Downloads, press enter.

Then type, jmol-14.29.42

Press enter.

Navigate to Jmol folder which we had downloaded and extracted earlier.


To do so, at the prompt type cd space Downloads, press Enter.


Then type cd space and the name of the Jmol folder. In my case, it is Jmol hyphen fourteen dot twenty-nine dot four two


You may have a different name depending on the version you have downloaded.


Press Enter.

Then type, java -jar Jmol.jar. Press enter. Then type java space hyphen jar space Jmol.jar


Press Enter.


Jmol Application interface opens.

Slide number 8

Installation on Linux OS


https://spoken-tutorial.org

Linux users can also install Jmol using Ubuntu Software Center or Synaptic Package Manager.


For information on how to use these, please see the Linux series on this website.

Point to Jmol menu bar and toolbar.


Back to Jmol interface.


Many features of Jmol are available in the menus on the menu bar and the toolbar.

Click on Help Menu.


Click on Jmol Wiki.


Close the page.

Click on Help menu.


Here we have link for Jmol Wiki main page.


Click on Jmol Wiki.


If you are connected to the internet Jmol Wiki main page opens in the web browser.

Cursor on the page. This page has detailed information about Jmol and Jsmol.


JSmol is a Java independent version of Jmol.

It runs in any HTML5 web browser.

Point to the links.


Point to all the sections.

This page has links to various pages on the left panel.


The page also has various sections for topics such as

  • About Jmol and JSmol,
  • Installation,
  • Development etc.
Cursor on Jmol/JSmol Community section.

Click on Community and Users link.

The section for Jmol Community has links to

Community and Users and Communities.


Click on Community and Users link.

Cursor on Community page.


Community page opens.

On this page you will find the work description of group of Jmol developers and Jmol users.

Cursor on sub-communities.

I will click on Crystal community.


Different web pages for various sub-communities are available here.

I will click on Crystal community.


Here Jmol users can discuss their experiences in using Jmol for displaying crystal structures.

Please explore these pages according to your interest.

Slide number 9

Advantages of Jmol Application

Advantages of Jmol Application.
  • No special hardware is required for high quality 3D-rendering.
  • If you are connected to internet you can directly

load models on Jmol panel from PubChem and PDB databases.

Slide Number 10

Uses of Jmol

Jmol can be effectively used to teach certain topics in Chemistry.

For example:

  • Structure and functional groups.
  • Atomic and Molecular orbitals.
  • Stereochemistry
  • Symmetry and point-groups.
  • Crystal structure and Unit cell.
Slide Number 11

Uses of Jmol Application

  • High quality 3D images can be produced,

they can be used in publications and presentations

  • View simulated proton and carbon 13 NMR spectra for molecules.
  • This feature is available in Jmol version 14.0 and above.
Slide Number 12

Uses of Jmol Application

Jmol can also be used to study
  • Structure Activity Relationships
  • Molecular modelling
  • Animation of molecules


Slide Number 13

Video Clippings

We have created a series of tutorials which describe how to use this software.
Slide Number 14

Introduction to Jmol Application


Show the tutorial clipping of Introduction to Jmol Application tutorial.

The first tutorial is Introduction to Jmol Application,


It explains various features available on Jmol window.


  • Create models of simple organic molecules.
  • Energy minimization and
  • Save image.

Here is the video clipping.

Slide Number 15

Create and Edit Molecular Models

Show the tutorial clipping of “Create and Edit” tutorial.

Next tutorial Create and Edit Molecular Models explains how to


  • Add functional group
  • Add and delete bonds
  • Add and delete atoms
  • Pop-up-menu.

Here is the video clipping.

Slide Number 16

Modify Display and View


Show the tutorial clipping of Modify Display and View tutorial.

Next tutorial Modify Display and View explains,
  • How to, modify the view.
  • Change the style of the display.
  • Save the image in various file formats.

Here is the video clipping.

Slide Number 17

Measurements and Labeling


Show the tutorial clipping of Measurements and labeling

Next tutorial Measurements and Labeling tutorial explains,


  • How to measure bond lengths, bond angles and dihedral angles for a model.
  • Label atoms with symbols and number.

Here is the video clipping.

Slide Number 18

Script Console and Script Commands


Show the tutorial clipping of Script console and Script commands

Next tutorial Script Console and Script Commands explains


  • How to use script console and write script commands.

Here is the video clipping.

Slide Number 19

Surfaces and Orbitals


Show the tutorial clipping of Surface and orbitals.

Next tutorial Surfaces and Orbitals demonstrates how to-


  • show surfaces, create models of aromatic molecules, atomic orbitals and molecular orbitals.

Here is the video clipping.

Slide number 20

Structures from Database


Show the tutorial clipping of “Structures from Database”

Next tutorial Structures from Database explains-


  • How to load structures directly from chemical structure database such as PubChem.
  • Convert 2D structures drawn in GChemPaint to 3D models in Jmol

Here is the video clipping.

Slide number 21

Crystal structure and Unit Cell


Show the tutorial clipping of

Crystal structure and Unit Cell

Next tutorial Crystal structure and Unit Cell shows demonstration of-


  • Download and open CIF files in Jmol.
  • Display unit cell and unit cell parameters.
  • Display crystal structures of different crystal systems.

Here is the video clipping.

Slide number 22

Proteins and macromolecules

Show the tutorial clipping of Proteins and macromolecules and “3D models of Enzymes”

Next tutorial, Proteins and macromolecules tutorial demonstrates how to


  • Download pdb files from database.
  • View and modify secondary structure of a protein.

Here is the video clipping of this tutorial.

Slide number 23

3D Models of Enzymes


Show the tutorial clipping of “Plane of symmetry and point-groups”

Next tutorial 3D Models of Enzymes explains how to-


  • Modify the display of secondary structure.
  • Highlight amino acid residues and substrate.
  • View Ramachandran plot for proteins.

Here is the video clipping of this tutorial.

Slide number 24

Symmetry and Point Groups

Show the tutorial clipping of Symmetry and Point Groups

Next tutorial Symmetry and Point Groups demonstrates
  • C2 and C3 rotational axes, reflection planes and point group classification.

Here is the video clipping

Slide number 25

Animation using Script Commands


Show the tutorial clipping of Animation using Script Commands

Next tutorial Animation using Script Commands demonstrates


  • Animation using script commands.
  • Save the animation as GIF file.

Here is the video clipping

Slide Number 26

Summary

Let us summarize,

In this tutorial we have learnt,

  • About Jmol Application.
  • Download and run Jmol Application on Linux OS.
  • Uses and advantages.
  • Play video clippings of Jmol Application tutorials available on our website.
Slide Number 27

Assignment

As an assignment-

1. Explore Jmol Application interface.

2. On the Jmol Wiki main page, explore Jmol Documentation page.

Slide Number 28

About Spoken Tutorial project

The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

Slide Number 29

Spoken Tutorial workshops

The Spoken Tutorial Project team:
  • conducts workshops using spoken tutorials and</nowiki>
  • gives certificates on passing online tests.</nowiki>

For more details, please write to us.

Slide Number 30

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 31

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 32

Acknowledgement

Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at

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Slide number 32 This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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