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

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|-
 
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|00:01
 
|00:01
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|Hello everyone.
+
|Hello everyone,Welcome to this tutorial on '''Introduction to Jmol Application'''.
−
 
+
−
|-
+
−
|00:02
+
−
|Welcome to this tutorial on '''Introduction to Jmol Application'''.
+
  
 
|-
 
|-
 
|00:07
 
|00:07
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|In this tutorial, I will briefly explain about:
+
|In this tutorial, I will briefly explain about
  
 
|-
 
|-
 
|00:11
 
|00:11
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|'''Jmol''' Application window and some basic operations.
+
|'''Jmol Application''' '''window''' and some basic operations.
  
 
|-
 
|-
 
|00:16  
 
|00:16  
−
|We will learn about
+
|We will learn about:
  
 
|-
 
|-
 
|00:18
 
|00:18
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|'''Menu Bar, Tool bar''', and '''Jmol''' panel.
+
|'''Menu bar, Tool bar''' and ''''Jmol' panel'''
  
 
|-
 
|-
 
|00:22
 
|00:22
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|How to: * Modify the size of '''Jmol''' panel.
+
|How to modify the size of '''Jmol''' panel
  
 
|-
 
|-
 
|00:25
 
|00:25
−
|* Create models of simple organic molecules.  
+
|Create models of simple organic molecules.  
  
 
|-
 
|-
−
| 00:28
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|00:28
−
|* Build molecules by substituting '''hydrogen''' with a '''Methyl''' group.
+
|Build molecules by substituting '''hydrogen''' with a '''Methyl''' group.
  
 
|-
 
|-
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|-
 
|-
 
|00:36
 
|00:36
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|* To Minimize energy to get a stable conformation  
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|to Minimize energy to get a stable conformation  
  
 
|-
 
|-
 
|00:41
 
|00:41
−
|and * Save the image as '''.mol''' file.
+
|and '''Save''' the image as '.mol' file.
  
 
|-
 
|-
 
|00:45
 
|00:45
−
|To follow this tutorial, you should have knowledge of  
+
|To follow this tutorial, you should have knowledge of:
  
 
|-
 
|-
 
|00:49
 
|00:49
−
|* High school Chemistry and  
+
|High school Chemistry and Basic Organic Chemistry.
−
 
+
−
|-
+
−
|00:50 
+
−
|* Basic Organic Chemistry  
+
  
 
|-
 
|-
 
|00:53
 
|00:53
−
|To record this tutorial I am using:
+
|To record this tutorial, I am using:
  
 
|-
 
|-
 
|00:56   
 
|00:56   
−
|* '''Ubuntu''' Operating System version. 12.04
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|'''Ubuntu''' Operating System version. 12.04
 +
 
 
|-
 
|-
−
 
 
|01:00   
 
|01:00   
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|* '''Jmol''' version 12.2.2  
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|'''Jmol''' version 12.2.2  
  
 
|-
 
|-
 
|01:03   
 
|01:03   
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|and * '''Java''' version 7  
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|and '''Java''' version 7.
  
 
|-
 
|-
 
|01:06  
 
|01:06  
−
|Please note.
+
|Please note-for '''Jmol''' Application''' to run smoothly, you should have '''Java '''installed on your system.
−
 
+
−
|-
+
−
|01:07 
+
−
|For '''Jmol '''Application to run smoothly, you should have '''Java '''installed on your system.
+
  
 
|-
 
|-
 
|01:14
 
|01:14
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|About '''Jmol Application.'''
+
|About '''Jmol Application-'''
  
 
|-
 
|-
 
|01:17   
 
|01:17   
−
|It is, * A free and open source '''Molecular Viewer.'''
+
|It is: * A free and open source '''Molecular Viewer'''.
  
 
|-
 
|-
 
|01:21   
 
|01:21   
−
|* Used to create and view 3 dimensional models of chemical structures.  
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|Used to create and view 3 dimensional models of chemical structures.  
  
 
|-
 
|-
 
|01:27  
 
|01:27  
−
|And also * Used to view secondary structures of '''proteins''' and '''macromolecules'''.
+
|And also used to view secondary structures of '''proteins''' and '''macromolecules'''.
  
 
|-
 
|-
 
|01:33
 
|01:33
−
|Information regarding Download and Installation
+
|Information regarding download and installation-
  
 
|-
 
|-
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|-
 
|-
 
|01:45   
 
|01:45   
−
|Please follow this tutorial in the '''Linux '''series on our website '''www.spoken-tutorial.org'''.
+
|Please follow this tutorial in the '''Linux '''series on our website:  www.spoken-tutorial.org
  
 
|-
 
|-
 
|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  
  
 
|-
 
|-
 
|02:08  
 
|02:08  
−
|And follow the instructions given on the web page to install.
+
|and follow the instructions given on the web page to install.
  
 
|-
 
|-
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|-
 
|-
 
|02:30
 
|02:30
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|Click on the '''Jmol '''icon to open the '''Jmol Application '''window.
+
|Click on the '''Jmol '''icon to open the '''Jmol''' Application window.
  
 
|-
 
|-
 
|02:35
 
|02:35
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|'''Jmol Application '''window has a '''menu bar''' at the top.
+
|'''Jmol Application '''window has a '''Menu bar''' at the top.
  
 
|-
 
|-
 
|02:40
 
|02:40
−
|Below the '''Menu bar''' there is a '''Tool bar'''.
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|Below the '''Menu bar''', there is a '''Tool bar'''.
  
 
|-
 
|-
 
|02:43
 
|02:43
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|Here is the '''Display area''', which is referred to as '''Jmol panel'''.
+
|Here is the '''Display area''' which is referred to as '''Jmol panel'''.
  
 
|-
 
|-
 
|02:48
 
|02:48
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|In the menu bar, there are various options like '''File, Edit, Display, '''etc'''.'''
+
|In the menu bar, there are various options like- '''File, Edit, Display '''etc.
  
 
|-
 
|-
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|03:18   
 
|03:18   
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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.
  
 
|-
 
|-
 
|03:23
 
|03:23
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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.
  
 
|-
 
|-
 
|03:27   
 
|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.
  
 
|-
 
|-
 
|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.  
  
 
|-
 
|-
 
|03:47   
 
|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 '''model'''s.
  
 
|-
 
|-
 
|03:53
 
|03:53
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|The '''Jmol panel''' can be resized, according to our requirement.  
+
|The '''Jmol panel''' can be resized according to our requirement.  
  
 
|-
 
|-
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|-
 
|-
 
|04:04
 
|04:04
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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.
  
 
|-
 
|-
 
|04:10
 
|04:10
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|'''Display''' menu in the '''menu bar''' can also be used to change the size of the panel.
+
|'''Display''' menu in the '''Menu bar''' can also be used to change the size of the '''panel'''.
  
 
|-
 
|-
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|-
 
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|04:20
 
|04:20
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|A dialog box opens, where we can specify the width and height dimensions, in '''pixels'''.
+
|A dialog-box opens where we can specify the width and height dimensions, in '''pixels'''.
  
 
|-
 
|-
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|-
 
|-
 
|04:32  
 
|04:32  
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|So I will type '''800 space 600''' and click on '''OK''' button.
+
|So, I will type '''800 space 600''' and click on the '''OK''' button.
  
 
|-
 
|-
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|-
 
|-
 
|05:12   
 
|05:12   
−
|Features of this menu include ability to * Easily add, delete, drag atoms.
+
|Features of this menu include ability to * Easily add, delete, drag atoms
  
 
|-
 
|-
 
|05:19   
 
|05:19   
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|* Add functional groups.
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|Add '''functional groups'''
  
 
|-
 
|-
 
|05:21   
 
|05:21   
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|* Delete, add and rotate bonds.
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|'''Delete, add''' and '''rotate''' bonds  
  
 
|-
 
|-
 
|05:25   
 
|05:25   
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|* Add Hydrogens, Minimize and save files. etc
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|'''add hydrogens, minimize''' and '''save files''' etc.
  
 
|-
 
|-
 
|05:30  
 
|05:30  
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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.  
  
 
|-
 
|-
 
|05:35  
 
|05:35  
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|The '''Modelkit''' function allows us to substitute a '''Hydrogen''' '''atom''' with a '''Methyl group'''.  
+
|The '''Modelkit''' function allows us to substitute a '''hydrogen''' atom with a '''Methyl group'''.  
  
 
|-
 
|-
 
|05:41  
 
|05:41  
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|Bring the cursor to the '''Hydrogen atom''' you want to substitute.
+
|Bring the cursor to the '''hydrogen''' atom, you want to substitute.
  
 
|-
 
|-
 
|05:46  
 
|05:46  
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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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|-
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|-
 
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|05:56  
 
|05:56  
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|'''Methane''' '''molecule''' is now converted to '''Ethane'''.
+
|'''Methane''' molecule is now converted to '''Ethane'''.
  
 
|-
 
|-
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|-
 
|-
 
|06:03   
 
|06:03   
−
|Click on the '''hydrogen atom''' to get a model of '''Propane'''.
+
|Click on the '''hydrogen''' atom to get a model of '''Propane'''.
  
 
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|-
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|06:13   
 
|06:13   
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|To do '''Energy minimization:'''
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|To do '''Energy minimization'''-
  
 
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|06:22   
 
|06:22   
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|We now have the model of the most stable conformation of '''Propane molecule. '''
+
|We now have the model of the most stable conformation of '''Propane''' molecule.
  
 
|-
 
|-
 
|06:28  
 
|06:28  
−
|To save this structure as a '''.mol''' file, open the '''Modelkit menu'''.
+
|To save this structure as a '.mol' file, open the '''Modelkit menu'''.
  
 
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|06:37   
 
|06:37   
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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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|06:54   
 
|06:54   
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|Go to the '''File Name '''and type '''Propane''' in the text box.
+
|Go to the '''File Name '''and type '''propane''' in the text-box.
  
 
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|-
 
|-
 
|07:03
 
|07:03
−
|Now, click on the '''Save''' button at the bottom right of the dialog box.
+
|Now, click on the '''Save''' button at the bottom right of the '''dialog-box'''.
  
 
|-
 
|-
 
|07:08  
 
|07:08  
−
|'''3D '''model of '''Propane''' will be saved as '''.mol''' file on the '''Desktop'''.
+
|'''3D '''model of '''Propane''' will be saved as '.mol' file on the '''Desktop'''.
  
 
|-
 
|-
 
|07:14   
 
|07:14   
−
|To exit '''Jmol''', click on the '''File''' menu and select '''Exit '''option, to exit the program.
+
|To exit '''Jmol''': click on the '''File''' menu and select '''Exit '''option to exit the program.
  
 
|-
 
|-
 
|07:21  
 
|07:21  
−
|Let's summarize.
+
|Let's summarize.In this tutorial, we learnt :
−
 
+
−
|-
+
−
|07:22 
+
−
|In this tutorial we learnt :
+
  
 
|-
 
|-
 
|07:25  
 
|07:25  
−
|* About '''Jmol Application '''window.
+
|About '''Jmol Application '''window.
  
 
|-
 
|-
 
|07:27  
 
|07:27  
−
|* Resize the '''Jmol panel.'''
+
|To resize the '''Jmol panel.'''
  
 
|-
 
|-
 
|07:29   
 
|07:29   
−
|* Use the '''Modelkit''' function in the Tool bar to create '''3D models''' of simple organic molecules like '''Methane, Ethane and Propane.'''  
+
|To use the '''Modelkit''' function in the Tool bar to create '''3D models''' of simple organic molecules like '''Methane, Ethane''' and '''Propane.'''  
 +
 
 
|-
 
|-
 
|07:40  
 
|07:40  
−
|* Build molecules by substitution of '''Hydrogen''' with '''Methyl group.'''
+
|Build molecule by substitution of '''hydrogen''' with '''methyl group.'''
  
 
|-
 
|-
 
|07:45  
 
|07:45  
−
|* Energy minimization to get a stable conformation.
+
|Energy minimization to get a stable conformation.
  
 
|-
 
|-
 
|07:48   
 
|07:48   
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|* And save the image as '''.mol''' file  
+
|And save the image as '''.mol''' file.
  
 
|-
 
|-
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|07:58   
 
|07:58   
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|* '''2-4 Dimethyl Pentane''' and '''3-Ethyl, 5-Methyl Heptane.'''
+
|'''2-4 Dimethyl Pentane''' and '''3-Ethyl, 5-Methyl Heptane.'''
  
 
|-
 
|-
 
|08:03   
 
|08:03   
−
|* Minimize the energy to get a stable conformation.  
+
|Minimize the energy to get a stable conformation.  
  
 
|-
 
|-
 
|08:07  
 
|08:07  
−
|* Save the image as '''.mol '''file.  
+
|Save the image as '''.mol''' file.  
  
 
|-
 
|-
 
|08:11   
 
|08:11   
−
|* Rotate the model using the '''rotate molecule''' in the tool bar.  
+
|Rotate the model using the '''rotate molecule''' in the tool bar.  
  
 
|-
 
|-
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|08:19   
 
|08:19   
−
|Watch the video available at the following link. '''http://spoken-tutorial.org/What http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial'''
+
|Watch the video available at the following link:http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
  
 
|-
 
|-
 
|08:22  
 
|08:22  
−
|It summarizes the Spoken Tutorial project.
+
|It summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
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|-
 
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|08:30  
 
|08:30  
−
|The Spoken Tutorial Project Team Conducts workshops using spoken tutorials.
+
|The '''Spoken Tutorial''' project team: * Conducts workshops using spoken tutorials.
  
 
|-
 
|-
 
|08:36   
 
|08:36   
−
|Gives certificates to those who pass an on-line test .
+
|Gives certificates to those who pass an on-line test.
  
 
|-
 
|-
 
|08:40   
 
|08:40   
−
|For more details, please write to '''contact@spoken-tutorial.org'''
+
|For more details, please write to: '''contact@spoken-tutorial.org'''
  
 
|-
 
|-
 
|08:47   
 
|08:47   
−
|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   
−
|It is supported by the National Mission on Education through ICT, MHRD, Government of India
+
|It is supported by the National Mission on Education through ICT, MHRD, Government of India.
  
 
|-
 
|-
 
|08:59   
 
|08:59   
−
|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   
−
|This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 15:33, 28 March 2017

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.

Contributors and Content Editors

Gaurav, PoojaMoolya, Pratik kamble, Sandhya.np14

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