Difference between revisions of "Jmol-Application/C2/Introduction-to-Jmol-Application/English-timed"

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|We will learn about
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|We will learn about:
  
 
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| '''Menu Bar, Tool bar''' and ''''Jmol' panel'''.
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|* '''Menu bar, Tool bar''' and ''''Jmol' panel'''.
  
 
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|How to: * Modify the size of '''Jmol''' panel.
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|* How to modify the size of '''Jmol''' panel.
  
 
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|* To Minimize energy to get a stable conformation  
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|To Minimize energy to get a stable conformation  
  
 
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|and * '''Save''' the image as ''''.mol'''' file.
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|and '''Save''' the image as ''''.mol'''' file.
  
 
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|for '''Jmol '''Application to run smoothly, you should have '''Java '''installed on your system.
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|for ''''Jmol' Application''' to run smoothly, you should have '''Java '''installed on your system.
  
 
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|And also * Used to view secondary structures of '''proteins''' and '''macromolecules'''.
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|And also used to view secondary structures of '''proteins''' and '''macromolecules'''.
  
 
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|Please follow this tutorial in the '''Linux '''series on our website '''www.spoken-tutorial.org'''.
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|Please follow this tutorial in the '''Linux '''series on our website:  www.spoken-tutorial.org
  
 
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|01:56   
 
|01:56   
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|For installation on Windows, Mac OS and Android devices, please visit:  '''www.jmol.sourceforge.net'''
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|For installation on Windows, Mac OS and Android devices, please visit:  www.jmol.sourceforge.net  
  
 
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|And follow the instructions given on the web page to install.
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|and follow the instructions given on the web page to install.
  
 
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|Click on the '''Jmol '''icon to open the '''Jmol Application '''window.
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|Click on the '''Jmol '''icon to open the '''Jmol''' Application window.
  
 
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|02:35
 
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|'''Jmol Application '''window has a '''menu bar''' at the top.
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|'''Jmol Application '''window has a '''Menu bar''' at the top.
  
 
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|In the menu bar, there are various options like- '''File, Edit, Display, '''etc.
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|In the menu bar, there are various options like- '''File, Edit, Display '''etc.
  
 
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|It also has a user guide which contains the documentation.
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|It also has a '''User Guide''' which contains the documentation.
  
 
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|The menu icons execute certain functions quickly; for e.g.- '''open, save, export, print''' etc.
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|The menu icons execute certain functions quickly; for e.g.- '''Open, Save, Export, Print''' etc.
  
 
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|'''“ modelkit”''' icon is used to create and edit molecular models.  
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|'''“ modelkit”''' icon is used to create and '''edit''' molecular '''model'''s.  
  
 
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|Now resize the window by dragging diagonally upwards or downwards.
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|Now, resize the window by dragging diagonally upwards or downwards.
  
 
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|04:10
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|'''Display''' menu in the '''menu bar''' can also be used to change the size of the '''panel'''.
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|'''Display''' menu in the '''Menu bar''' can also be used to change the size of the '''panel'''.
  
 
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|A dialog box opens where we can specify the width and height dimensions, in '''pixels'''.
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|A dialog-box opens where we can specify the width and height dimensions, in '''pixels'''.
  
 
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|So, I will type '''800 space 600''' and click on '''OK''' button.
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|So, I will type '''800 space 600''' and click on the '''OK''' button.
  
 
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|Features of this menu include ability to * Easily add, delete, drag atoms.
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|Features of this menu include ability to * Easily add, delete, drag atoms
  
 
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|* Add functional groups.
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|* Add '''functional groups'''
  
 
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|* Delete, add and rotate bonds.
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|* '''Delete, add''' and '''rotate''' bonds  
  
 
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|* Add Hydrogens, Minimize and save files etc.
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|* '''add hydrogens, minimize''' and '''save files''' etc.
  
 
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|The '''Modelkit''' function allows us to substitute a '''Hydrogen''' atom with a '''Methyl group'''.  
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|The '''Modelkit''' function allows us to substitute a '''hydrogen''' atom with a '''Methyl group'''.  
  
 
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|Bring the cursor to the '''Hydrogen''' atom you want to substitute.
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|Bring the cursor to the '''hydrogen''' atom you want to substitute.
  
 
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|A red ring appears on that '''Hydrogen''' atom.
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|A red ring appears on that '''hydrogen''' atom.
  
 
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|Click on the '''Hydrogen''' atom to get a model of '''Propane'''.
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|Click on the '''hydrogen''' atom to get a model of '''Propane'''.
  
 
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|To do '''Energy minimization,'''-
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|To do '''Energy minimization'''-
  
 
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|To save this structure as a '''.mol''' file, open the '''Modelkit menu'''.
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|To save this structure as a '.mol' file, open the '''Modelkit menu'''.
  
 
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|A '''Save''' dialog box appears on the screen.
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|A '''Save''' dialog-box appears on the screen.
  
 
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|Go to the '''File Name '''and type '''Propane''' in the text box.
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|Go to the '''File Name '''and type '''propane''' in the text-box.
  
 
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|Now, click on the '''Save''' button at the bottom right of the '''dialog box'''.
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|Now, click on the '''Save''' button at the bottom right of the '''dialog-box'''.
  
 
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|'''3D '''model of '''Propane''' will be saved as '''.mol''' file on the '''Desktop'''.
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|'''3D '''model of '''Propane''' will be saved as '.mol' file on the '''Desktop'''.
  
 
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|* Resize the '''Jmol panel.'''
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|* To resize the '''Jmol panel.'''
  
 
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|* Use the '''Modelkit''' function in the Tool bar to create '''3D models''' of simple organic molecules like '''Methane, Ethane and Propane.'''  
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|* To use the '''Modelkit''' function in the Tool bar to create '''3D models''' of simple organic molecules like '''Methane, Ethane''' and '''Propane.'''  
 
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|* Build molecules by substitution of '''Hydrogen''' with '''Methyl group.'''
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|* Build molecule by substitution of '''hydrogen''' with '''methyl group.'''
  
 
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|* And save the image as '''.mol''' file.  
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|* And save the image as '.mol' file.  
  
 
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|Watch the video available at the following link: '''http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial'''
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|Watch the video available at the following link: http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
  
 
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|The Spoken Tutorial Project team: * conducts workshops using spoken tutorials.
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|The Spoken Tutorial Project team: * Conducts workshops using spoken tutorials.
  
 
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|More information on this mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro'''
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|More information on this mission is available at this link: http://spoken-tutorial.org/NMEICT-Intro
  
 
|-
 
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|09:04   
 
|09:04   
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|This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
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|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
  
 
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Revision as of 23:50, 6 October 2015

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

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