Jmol-Application/C2/Introduction-to-Jmol-Application/English-timed
From Script | Spoken-Tutorial
| Time | Narration |
| 00:01 | Hello everyone,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 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-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.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. |
