Jmol-Application/C2/Overview-of-Jmol-Application/English-timed
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00:01 | Welcome to this Overview tutorial on Jmol Application series. |
00:06 | In this tutorial we will go through, |
00:09 | Important features of Jmol Application. |
00:12 | Information regarding download and installation on various operating systems. |
00:18 | Uses of Jmol Application. |
00:21 | We will Play clippings of video tutorials available in Jmol Application series at our website. |
00:29 | To follow this tutorial you should have knowledge of, High School chemistry Or Basic Organic Chemistry |
00:37 | To record this tutorial, I am using, Ubuntu OS version 12.10 |
00:43 | Jmol version 14.1.11
Java version 7 and Mozilla Firefox Browser 35.0 |
00:53 | About Jmol Application,
Jmol is a molecular viewer for three-dimensional chemical structures and macromolecules.
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01:02 | Jmol can be used to create and edit 3D models of chemical structures. |
01:08 | This software can be used by students, educators, and researchers in chemistry and biochemistry. |
01:16 | Here are some important features of Jmol. |
01:19 | It is a Free and Open Source Software. |
01:22 | Works on Windows, Mac Operating System, Linux and also on android devices. |
01:30 | It supports all major web browsers. |
01:33 | No special hardware is required for high quality 3D-rendering. |
01:38 | Images can be exported to various file formats: Such as jpg, png, gif, pdf etc. |
01:47 | Reads various file formats such as pdb, cif, mol, cml, xyz etc |
01:56 | If you are connected to internet you can directly loads models on Jmol panel: |
02:02 | From databases such as pubchem for chemical structures. |
02:07 | And PDB database for proteins and macromolecules. |
02:12 | More information about this software is available at the following links.
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02:18 | Uses of Jmol :
Jmol can be used as a teaching tool to explain concepts in chemistry. |
02:26 | And for producing high quality 3D images that can be used in print media:
such as journals, publications and books. |
02:36 | And also for presentations in classrooms and lectures. |
02:41 | Jmol can also be used for molecular modelling and producing animation movies. |
02:48 | Here is the webpage that describes how to incorporate Jmol images in powerpoint presentations. |
02:56 | Jmol can be effectively used to teach certain topics in chemistry which require 3D visualization. |
03:03 | At Basic level, topics such as: Structure and functional groups. |
03:08 | Atomic and Molecular orbitals. |
03:11 | 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. |
03:22 | Symmetry and point-groups. Crystal Structure and Unit cell. |
03:27 | And Predict proton NMR spectrum for molecules. |
03:31 | This feature available in Jmol version 14.0 and above. |
03:36 | Jmol can be used to study Structure Activity Relationships. |
03:41 | Lets see how to download and install Jmol. |
03:44 | Jmol can be installed on Windows, Mac operating system and on Linux systems. |
03:51 | A special version of Jmol for Android devices is available at the link shown below. |
03:57 | For Linux operating systems, download using Ubuntu software center or Synaptic package manager. |
04:04 | Follow this tutorial in the linux series on our website. |
04:08 | For Windows and Mac operating systems: Open the given link in any web browser. |
04:15 | I will open this link and quickly go through the contents given on the web-page. |
04:20 | This web-page gives a lot of general information about Jmol. Scroll down the page. |
04:27 | It gives information about the overview, demonstration pages, features. |
04:35 | To download Jmol click on the downloads page. Follow the instructions given on the page to download. |
04:44 | Information about installing and running Jmol is also given on this page. |
04:50 | I have created a series of tutorials which describe how to use this software. |
04:56 | The first tutorial Introduction to Jmol Application has information regarding the various features available on Jmol window. |
05:04 | Here is the video clipping of that video. |
05:07 | |
05:13 | To create and edit molecular models, follow the tutorial Create and Edit.
Here is the clipping. |
05:18 | ---- Add Video Clip------ |
05:27 | We can Measure bond lengths, bond angles and dihedral angles. Here is the video clipping. |
05:34 | |
05:40 | Using Jmol we can show surfaces and create atomic and molecular orbitals.
Here is the video clipping. |
05:47 | |
05:56 | This video explains how to show Plane of symmetry and point-groups.
Here is the video clipping. |
06:02 | |
06:09 | Crystal structures and unit cell can be viewed using Jmol. Here is the video clipping. |
06:17 | |
06:24 | Here is the video clipping to show proteins and macromolecules in Jmol. |
06:29 | |
06:37 | A simulated H NMR spectrum can be displayed for all the molecules listed in chemical structure database: Starting from Jmol version 14.0 |
06:49 | Let me open Jmol window and demonstrate this feature. |
06:54 | To view simulated proton NMR: Go to tools menu. |
06:59 | Scroll down to spectra and click on spectrum |
07:04 | The Jspecview window opens. |
07:08 | Scroll down the file menu, click on add simulation |
07:13 | In the dialog box enter the name of the molecule. |
07:17 | Let us type nitrobenzene, click on ok button. |
07:22 | A proton NMR spectrum of nitrobenzene is displayed on the panel. |
07:28 | Atoms on the structure are correlated with signals in the spectrum. |
07:33 | Certain files include information about molecular vibrations, such as GAMESS .log files and Spartan output files. |
07:45 | We can open these files in Jmol and view vibrations. |
07:50 | Let me open a log file showing vibrations in carbondioxide molecule. |
08:00 | Here is an animation, showing vibrations in benzene molecule. |
08:05 | Here is the animation showing conformations in cyclohexane molecule. |
08:15 | Let us summarize, In this tutorial we have learnt, |
08:19 | Important features of Jmol Application. |
08:22 | Information regarding Installation on various operating systems.
Uses of Jmol Application. |
08:29 | We have also seen clippings of video tutorials in Jmol Application series. |
08:35 | And some animation videos showing vibrations and conformations of cyclohexane. |
08:42 | The video at the following link summarizes the Spoken Tutorial project.
Please download and watch it. |
08:48 | The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.
For more details, please write to us. |
08:59 | Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
More information on this Mission is available at the link shown. |
09:09 | This is Snehalatha from IIT Bombay signing off. Thank you for joining. |