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

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|'''Jmol''' Application window and some basic operations.
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|''''Jmol' Application''' '''window''' and some basic operations.
  
 
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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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|We will also learn  
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|We will also learn:
  
 
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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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|To follow this tutorial, you should have knowledge of  
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|To follow this tutorial, you should have knowledge of:
  
 
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|* Basic Organic Chemistry  
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|* Basic Organic Chemistry.
  
 
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|To record this tutorial I am using:
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|To record this tutorial, I am using:
  
 
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|Please note.
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|Please note-
  
 
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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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|About '''Jmol Application.'''
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|About '''Jmol Application-'''
  
 
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|It is, * A free and open source '''Molecular Viewer.'''
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|It is: * A free and open source '''Molecular Viewer'''.
  
 
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|Information regarding Download and Installation  
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|Information regarding Download and Installation-
  
 
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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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|Below the '''Menu bar''' there is a '''Tool bar'''.
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|Below the '''Menu bar''', there is a '''Tool bar'''.
  
 
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|Here is the '''Display area''', which is referred to as '''Jmol panel'''.
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|Here is the '''Display area''' which is referred to as '''Jmol panel'''.
  
 
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|02:48
 
|02:48
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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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|'''Tool bar '''has a number of menu icons.
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|'''Tool bar '''has a number of menu '''icon'''s.
  
 
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|03:27   
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|The menu icons execute certain functions quickly; for eg 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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|03:37
 
|03:37
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|Here is a set of icons to rotate, select a set of atoms, measure distances, etc.  
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|Here is a set of icons- to rotate, select a set of atoms, measure distances etc.  
  
 
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|03:47   
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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 models.
  
 
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|The '''Jmol panel''' can be resized, according to our requirement.  
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|The '''Jmol panel''' can be resized according to our requirement.  
  
 
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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 '''OK''' button.
  
 
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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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|To use a particular feature on the menu, click on the check box provided.  
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|To use a particular feature on the menu, click on the check-box provided.  
  
 
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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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|'''Methane''' '''molecule''' is now converted to '''Ethane'''.
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|'''Methane''' molecule is now converted to '''Ethane'''.
  
 
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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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|We now have the model of the most stable conformation of '''Propane molecule. '''
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|We now have the model of the most stable conformation of '''Propane''' molecule.
  
 
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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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|To exit '''Jmol''', click on the '''File''' menu and select '''Exit '''option, to exit the program.
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|To exit '''Jmol''', click on the '''File''' menu and select '''Exit '''option to exit the program.
  
 
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|In this tutorial we learnt :
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|In this tutorial, we learnt :
  
 
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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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|* Save the image as '''.mol '''file.  
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|* Save the image as ''''.mol''''file.  
  
 
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|Watch the video available at the following link. '''http://spoken-tutorial.org/What 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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|It summarizes the Spoken Tutorial project.
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|It summarizes the '''Spoken Tutorial''' project.
  
 
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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.
  
 
|-
 
|-
 
|08:36   
 
|08:36   
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|Gives certificates to those who pass an on-line test .
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|* Gives certificates to those who pass an on-line test.
  
 
|-
 
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|08:40   
 
|08:40   
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|For more details, please write to '''contact@spoken-tutorial.org'''
+
|For more details, please write to: '''contact@spoken-tutorial.org'''
  
 
|-
 
|-
 
|08:47   
 
|08:47   
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|Spoken Tutorial Project is a part of the Talk to a Teacher project  
+
|'''Spoken Tutorial''' project is a part of the '''Talk to a Teacher''' project.
  
 
|-
 
|-
 
|08:52   
 
|08:52   
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|It is supported by the National Mission on Education through ICT, MHRD, Government of India
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|It is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
|-
 
|08:59   
 
|08:59   
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|More information on this Mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro'''
+
|More information on this mission is available at this link '''http://spoken-tutorial.org/NMEICT-Intro'''
  
 
|-
 
|-
 
|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.  
  
 
|}
 
|}

Revision as of 19:48, 13 September 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 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]_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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