Jmol-Application/C2/Introduction-to-Jmol-Application/English-timed

Time	Narration
00:01	Hello everyone.
00:02	Welcome to this tutorial on Introduction to Jmol Application.
00:07	In this tutorial, I will briefly explain about:
00:11	'Jmol' Application window and some basic operations.
00:16	We will learn about:
00:18	* Menu bar, Tool bar and 'Jmol' panel.
00:22	* How to modify the size of Jmol panel.
00:25	* Create models of simple organic molecules.
00:28	* Build molecules by substituting hydrogen with a Methyl group.
00:34	We will also learn:
00:36	To Minimize energy to get a stable conformation
00:41	and Save the image as '.mol' file.
00:45	To follow this tutorial, you should have knowledge of:
00:49	* High school Chemistry and
00:50	* Basic Organic Chemistry.
00:53	To record this tutorial, I am using:
00:56	* Ubuntu Operating System version. 12.04
01:00	* Jmol version 12.2.2
01:03	and * Java version 7.
01:06	Please note-
01:07	for 'Jmol' Application to run smoothly, you should have Java installed on your system.
01:14	About Jmol Application-
01:17	It is: * A free and open source Molecular Viewer.
01:21	* Used to create and view 3 dimensional models of chemical structures.
01:27	And also used to view secondary structures of proteins and macromolecules.
01:33	Information regarding Download and Installation-
01:37	For Ubuntu OS, installation of Jmol is done using Ubuntu Software Center.
01:45	Please follow this tutorial in the Linux series on our website: www.spoken-tutorial.org
01:56	For installation on Windows, Mac OS and Android devices, please visit: www.jmol.sourceforge.net
02:08	and follow the instructions given on the web page to install.
02:13	I have already installed Jmol Application on my system using Ubuntu Software Center.
02:20	To open the Jmol Application, click on Dash home.
02:24	Type Jmol in the search box.
02:27	Jmol icon appears on the screen.
02:30	Click on the Jmol icon to open the Jmol Application window.
02:35	Jmol Application window has a Menu bar at the top.
02:40	Below the Menu bar, there is a Tool bar.
02:43	Here is the Display area which is referred to as Jmol panel.
02:48	In the menu bar, there are various options like- File, Edit, Display etc.
02:56	Each of these have various sub-options as well.
03:00	Tools menu has tools to measure distances between atoms, apart from other options.
03:07	We will learn about these options in subsequent tutorials.
03:12	Help menu has a lot of useful information about Jmol Application.
03:18	It also has a User Guide which contains the documentation.
03:23	Tool bar has a number of menu icons.
03:27	The menu icons execute certain functions quickly; for e.g.- Open, Save, Export, Print etc.
03:37	Here is a set of icons- to rotate, select a set of atoms, measure distances etc.
03:47	“ modelkit” icon is used to create and edit molecular models.
03:53	The Jmol panel can be resized according to our requirement.
03:58	Take the cursor to any corner of the window till it changes to an arrow indicator.
04:04	Now, resize the window by dragging diagonally upwards or downwards.
04:10	Display menu in the Menu bar can also be used to change the size of the panel.
04:16	Click on Display menu and select Resize option.
04:20	A dialog-box opens where we can specify the width and height dimensions, in pixels.
04:27	I need a window of size 800 by 600 pixels.
04:32	So, I will type 800 space 600 and click on the OK button.
04:41	Now the Jmol panel is resized to 800 by 600 pixels.
04:47	Let's now proceed to create models of some simple organic molecules.
04:53	Modelkit allows us to build and modify models with energy minimization.
05:00	Click on the “modelkit” icon in the tool bar.
05:04	A model of Methane appears on the panel.
05:07	A menu appears on the top-left corner of the Jmol panel.
05:12	Features of this menu include ability to * Easily add, delete, drag atoms
05:19	* Add functional groups
05:21	* Delete, add and rotate bonds
05:25	* add hydrogens, minimize and save files etc.
05:30	To use a particular feature on the menu, click on the check-box provided.
05:35	The Modelkit function allows us to substitute a hydrogen atom with a Methyl group.
05:41	Bring the cursor to the hydrogen atom you want to substitute.
05:46	A red ring appears on that hydrogen atom.
05:50	Click on the atom.
05:52	You will notice that a Methyl group has been added.
05:56	Methane molecule is now converted to Ethane.
06:00	Repeat the same step as before.
06:03	Click on the hydrogen atom to get a model of Propane.
06:07	Energy minimization on this molecule will give us the most stable conformation.
06:13	To do Energy minimization-
06:15	Scroll down the options in the Modelkit menu.
06:19	Click on the option minimize.
06:22	We now have the model of the most stable conformation of Propane molecule.
06:28	To save this structure as a '.mol' file, open the Modelkit menu.
06:33	Scroll down the menu and click on save file option.
06:37	A Save dialog-box appears on the screen.
06:41	Click on the folder where you want to save your file.
06:45	I am choosing Desktop as the location for saving my file.
06:50	So, select Desktop and click on the Open button.
06:54	Go to the File Name and type propane in the text-box.
06:59	Click on Files of Type and select MOL option.
07:03	Now, click on the Save button at the bottom right of the dialog-box.
07:08	3D model of Propane will be saved as '.mol' file on the Desktop.
07:14	To exit Jmol, click on the File menu and select Exit option to exit the program.
07:21	Let's summarize.
07:22	In this tutorial, we learnt :
07:25	* About Jmol Application window.
07:27	* To resize the Jmol panel.
07:29	* To use the Modelkit function in the Tool bar to create 3D models of simple organic molecules like Methane, Ethane and Propane.
07:40	* Build molecule by substitution of hydrogen with methyl group.
07:45	* Energy minimization to get a stable conformation.
07:48	* And save the image as '.mol' file.
07:52	Using the Jmol Modelkit function, make models of the following molecules:
07:58	* 2-4 Dimethyl Pentane and 3-Ethyl, 5-Methyl Heptane.
08:03	* Minimize the energy to get a stable conformation.
08:07	* Save the image as '.mol'file.
08:11	* Rotate the model using the rotate molecule in the tool bar.
08:15	Your completed assignment should look as follows.
08:19	Watch the video available at the following link: http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
08:22	It summarizes the Spoken Tutorial project.
08:26	If you do not have good bandwidth, you can download and watch it.
08:30	The Spoken Tutorial Project team: * Conducts workshops using spoken tutorials.
08:36	* Gives certificates to those who pass an on-line test.
08:40	For more details, please write to: contact@spoken-tutorial.org
08:47	Spoken Tutorial project is a part of the Talk to a Teacher project.
08:52	It is supported by the National Mission on Education through ICT, MHRD, Government of India.
08:59	More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro
09:04	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

Gaurav, PoojaMoolya, Pratik kamble, Sandhya.np14