View source for Jmol-Application/C2/Overview-of-Jmol-Application/English

{| style="border-spacing:0;"
! <center>Visual Cue</center>
! <center>Narration</center>

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| 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'''

'''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.

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| 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'''

'''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, 


Important features of Jmol Application.


Information regarding download and installation on various operating systems.


Uses of Jmol Application.


We will Play clippings of video tutorials available in Jmol Application series at our website.

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| 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'''

'''Pre-requisites'''
| 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


Or Basic Organic Chemistry

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| 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'''

'''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

'''Java''' version 7

and Mozilla Firefox Browser 35.0

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| 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'''

'''What is 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;"| About Jmol Application,

Jmol is a molecular viewer for three-dimensional chemical structures and macromolecules.


Jmol can be used to create and edit 3D models of chemical structures.


This software can be used by students, educators, and researchers in chemistry and biochemistry.

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| 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'''

'''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.


It is a Free and Open Source Software.


Works on Windows, Mac Operating System, Linux and also on android devices.


It supports all major web browsers.


No special hardware is required for high quality 3D-rendering.

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| 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'''

'''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;"| Images can be exported to various file formats: Such as 

jpg, png, gif, pdf etc.


Reads various file formats such as pdb, cif, mol, cml, xyz etc


If you are connected to internet you can directly 

loads models on Jmol panel:


From databases such as pubchem for chemical structures. 


And PDB database for proteins and macromolecules.

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| 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'''

'''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. 


http://jmol.sourceforge.net/

[http://www.jmol.org/ http://www.jmol.org/]


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| 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'''

'''Uses of 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;"| Uses of Jmol.

Jmol can be used:

as a teaching tool to explain concepts in chemistry.


And for producing high quality 3D images that can be used in print media:


such as journals, publications and books.


And also for presentations in classrooms and lectures.

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| 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'''
| 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.

And producing animation movies.

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| 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 

[http://www.umass.edu/molvis/bme3d/ http://www.umass.edu/molvis/bme3d/]

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.


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| 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'''

'''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.


At Basic level, topics such as:


Structure and functional groups.


Atomic and Molecular orbitals.

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| 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'''

'''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.


Symmetry and point-groups.


Crystal Structure and Unit cell.


And Predict proton NMR spectrum for molecules. 


This feature available in Jmol version 14.0 and above.


Jmol can be used to study Structure Activity Relationships.

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| 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'''

'''Download and Installation'''



| 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.


Jmol can be installed on Windows, Mac operating system and on Linux systems.


A special version of Jmol for Android devices is available at the link shown below. 


http://wiki.jmol.org/index.php/Support/Android


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| 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'''

'''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.


Follow this tutorial in the linux series on our website.

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| 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'''

'''Download and Installation'''

'''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.


[http://www.jmol.sourceforge.net/ www.][http://www.jmol.sourceforge.net/ jmol.][http://www.jmol.sourceforge.net/ sourceforge.net]


I will open this link and quickly go through the contents given on the web-page.

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| 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.


Scroll down the page.
| 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.


It gives information about the overview, demonstration pages, features.


To download Jmol click on the downloads page.


Follow the instructions given on the page to download.


Information about installing and running Jmol is also given on this page. 


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| 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'''

'''Video Clippings'''
| 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.




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| 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.


Click on the modelkit menu.


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. 


Here is the video clipping of that video.

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| 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.
| 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”.


Here is the clipping.


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| 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”
| 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. 


Here is the video clipping.

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| 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”
| 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.


Here is the video clipping.

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| 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” 



| 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.


Here is the video clipping.

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| 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”



| 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.

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| 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.

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| 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'''



| 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:


Starting from Jmol version 14.0


Let me open Jmol window and demonstrate this feature.

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| 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 


Go to tools menu, scroll down to “spectra”, then click on “proton spectra”.


Scroll down the file menu, click on “add simulation”.


In the dialog box, type “nitrobenzene”.


Click on ok button. 
| 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.

Scroll down to “spectra” and click on “spectrum”.


The Jspecview window opens. 


Scroll down the file menu, click on “add simulation”


In the dialog box enter the name of the molecule.


Let us type “nitrobenzene”, click on ok button. 


A proton NMR spectrum of nitrobenzene is displayed on the panel.


Atoms on the structure are correlated with signals in the spectrum.

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| 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'''

'''Animating Vibrations'''
| 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.

|-
| 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.

|-
| 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
| 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.

|-
| 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.

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| 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'''

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,

In this tutorial we have learnt,

Important features of Jmol Application.

Information regarding Installation on various operating systems.

Uses of Jmol Application.

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| 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'''

'''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;"| We have also seen clippings of video tutorials in Jmol Application series.

And some animation videos showing vibrations and conformations of cyclohexane.

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| 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'''

'''Acknowledgement '''
| 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. 

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 22'''
| 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. 

|-
| 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'''
| 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. 

More information on this Mission is available at the link shown. 

|-
| 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'''
| 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. 

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