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

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| Here are some important features of '''Jmol.'''
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|A proton NMR spectrum of nitrobenzene is displayed on the panel.
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|  The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us.  
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|  The '''Spoken Tutorial''' project team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us.  
  
 
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Revision as of 17:05, 1 June 2016

Time
Narration
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.

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 load 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.
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 power-point 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 is available in Jmol version 14.0 and above.
03:36 Jmol can be used to study Structure Activity Relationships.
03:41 Let's 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 Add Video clip.
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 Add Video clip.
05:40 Using Jmol, we can show surfaces and create atomic and molecular orbitals.

Here is the video clipping.

05:47 Add Video clip.
05:56 This video explains how to show Plane of symmetry and point-groups.

Here is the video clipping.

06:02 Add Video clip
06:09 Crystal structures and unit cell can be viewed using Jmol. Here is the video clipping.
06:17 Add Video clip
06:24 Here is the video clipping to show proteins and macromolecules in Jmol.
06:29 Add video clip
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 nitro benzene 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 carbon dioxide molecule.
08:00 Here is the animation video, 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.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14

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