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 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.
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.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14