Jmol-Application/C2/Overview-of-Jmol-Application/English
|
|
---|---|
Slide Number 1
Title Slide |
Welcome to this Overview tutorial on Jmol Application series. |
Slide Number 2
Learning Objectives |
In this tutorial we will go through,
|
Slide Number 3
Pre-requisites |
To follow this tutorial you should have knowledge of,
|
Slide Number 4
System Requirement |
To record this tutorial, I am using,
Ubuntu OS version 12.10 Jmol version 14.1.11 Java version 7 and Mozilla Firefox Browser 35.0 |
Slide Number 5
What is Jmol Application?
|
About Jmol Application,
Jmol is a molecular viewer for three-dimensional chemical structures and macromolecules.
|
Slide Number 6
Important Features |
Here are some important features of Jmol.
|
Slide Number 7
Important Features
|
Images can be exported to various file formats: Such as
jpg, png, gif, pdf etc.
loads models on Jmol panel:
|
Slide Number 8
Important Links |
More information about this software is available at the following links.
|
Slide Number 9
Uses of Jmol |
Uses of Jmol.
Jmol can be used: as a teaching tool to explain concepts in chemistry.
|
Slide Number 10
Uses of Jmol |
Jmol can also be used for molecular modelling.
And producing animation movies. |
Open the below link
http://www.umass.edu/molvis/bme3d/ materials/jtat_080510/_docs/slides.htm |
Here is the webpage that describes how to incorporate Jmol images in powerpoint presentations.
|
Slide Number 11
Teaching Chemistry using Jmol. |
Jmol can be effectively used to teach certain topics in chemistry which require 3D visualization.
|
Slide Number 12
Teaching Chemistry using Jmol. |
At advanced levels Jmol can be used to teach topics such as
|
Slide Number 13
Download and Installation
|
Lets see how to download and install Jmol.
|
Slide number 14
Download and Installation on Linux OS |
For Linux operating systems, download using Ubuntu software center or Synaptic package manager.
|
Slide number 15
Download and Installation for |
For Windows and Mac operating systems:
Open the given link in any web browser.
|
Cursor on web-page.
|
This web-page gives a lot of general information about Jmol.
Scroll down the page.
|
Slide Number 16
Video Clippings |
I have created a series of tutorials which describe how to use this software.
|
Cursor on menu bar and tool bar.
|
The first tutorial “Introduction to Jmol Application” has information regarding the various features available on Jmol window.
|
Show the tutorial clipping of “Create and Edit” tutorial. | To create and edit molecular models, follow the tutorial “Create and Edit”.
|
Show the tutorial clipping of “Measurements and labeling” | We can Measure bond lengths, bond angles and dihedral angles.
|
Show the tutorial clipping of “Surface and orbitals” | Using Jmol we can show surfaces and create atomic and molecular orbitals.
|
Show the tutorial clipping of “Plane of symmetry and point-groups”
|
This video explains how to show Plane of symmetry and point-groups.
|
Show the tutorial clipping of “Crystal structure and Unit Cell”
|
Crystal structures and unit cell can be viewed using Jmol.Here is the video clipping. |
Show the tutorial clipping of “Proteins and macromolecules” | Here is the video clipping to show proteins and macromolecules in Jmol. |
Slide number 17
Simulated H NMR
|
A simulated H NMR spectrum can be displayed for all the molecules listed in chemical structure database:
|
Cursor on the panel
|
To view simulated proton NMR:
Go to tools menu. Scroll down to “spectra” and click on “spectrum”.
|
Slide Number 18
Animating Vibrations |
Certain files include information about molecular vibrations, such as GAMESS .log files and Spartan output files.
|
Open the file CO2-DZV-hess.log | Let me open a log file showing vibrations in carbondioxide molecule. |
Open the file C6H6.smol | Here is an animation, showing vibrations in benzene molecule. |
Open the file cyclohexane_movie.xyz | Here is the animation showing conformations in cyclohexane molecule. |
Slide Number 19
Summary |
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. |
Slide Number 20
Summary |
We have also seen clippings of video tutorials in Jmol Application series.
And some animation videos showing vibrations and conformations of cyclohexane. |
Slide Number 21
Acknowledgement |
The video at the following link summarizes the Spoken Tutorial project.
Please download and watch it. |
Slide Number 22 | The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.
For more details, please write to us. |
Slide number 23 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
More information on this Mission is available at the link shown. |
Slide number 23 | This is Snehalatha from IIT Bombay signing off. Thank you for joining. |