Jmol-Application/C2/Overview-of-Jmol-Application/English-timed

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
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.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14