Difference between revisions of "Jmol-Application/C2/Introduction-to-Jmol-Application/English-timed"
From Script | Spoken-Tutorial
(Created page with '{| border=1 |'''Time''' |'''Narration''' |- |00:01 |Hello everyone. |- |00:02 |Welcome to this tutorial on '''Introduction to Jmol Application'''. |- |00:07 |In this tutorial,…') |
|||
| Line 118: | Line 118: | ||
|01:56 | |01:56 | ||
|For installation on Windows, Mac OS and Android devices, please visit '''www.jmol.sourceforge.net''' | |For installation on Windows, Mac OS and Android devices, please visit '''www.jmol.sourceforge.net''' | ||
| − | |||
|- | |- | ||
| Line 299: | Line 298: | ||
|06:00 | |06:00 | ||
|Repeat the same step as before. | |Repeat the same step as before. | ||
| − | |||
|- | |- | ||
| Line 336: | Line 334: | ||
|06:37 | |06:37 | ||
|A '''Save''' dialog box appears on the screen. | |A '''Save''' dialog box appears on the screen. | ||
| − | |||
|- | |- | ||
Revision as of 10:48, 8 August 2014
| 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 eg 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 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 | * Resize the Jmol panel. |
| 07:29 | * Use the Modelkit function in the Tool bar to create 3D models of simple organic molecules like Methane, Ethane and Propane. |
| 07:40 | * Build molecules 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 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. |
