Difference between revisions of "Jmol-Application/C2/Script-Console-and-Script-Commands/English-timed"

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| Welcome to this tutorial on '''Script console and script commands '''in '''Jmol Application'''.
+
|Welcome to this tutorial on '''Script console and script commands '''in '''Jmol Application'''.
  
 
|-
 
|-
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| 00:08
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|00:08
 
|In this tutorial, we will learn:  
 
|In this tutorial, we will learn:  
  
 
|-
 
|-
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|00:11
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|* About '''script commands'''
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|About '''script commands'''
  
 
|-
 
|-
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| 00:13
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|00:13
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|* How to use '''script console''' window
+
|How to use '''script console''' window
  
 
|-
 
|-
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| 00:16
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|00:16
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|* Change display of the model by using '''script commands'''
+
|Change display of the model by using '''script commands'''
  
 
|-
 
|-
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| 00:21
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|00:21
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|* Display lines of text on the '''panel'''.  
+
|Display lines of text on the '''panel'''.  
  
 
|-
 
|-
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| 00:24
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|00:24
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| To follow this tutorial,
+
|To follow this tutorial,
  
 
|-
 
|-
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| 00:26
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|00:26
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|you should know how to
+
|you should know how to,create and '''edit''' molecular models in '''Jmol Application'''.
  
 
|-
 
|-
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| 00:27
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|00:32
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| create and '''edit''' molecular models in '''Jmol Application'''.
+
−
 
+
−
|-
+
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| 00:32
+
 
|If not, watch the relevant tutorials available on our website.
 
|If not, watch the relevant tutorials available on our website.
  
 
|-
 
|-
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| 00:37
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|00:37
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| To record this tutorial, I am using:
+
|To record this tutorial, I am using:
  
 
|-
 
|-
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| 00:39
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|00:39
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| * '''Ubuntu '''OS version 12.04
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|'''Ubuntu '''OS version 12.04
  
 
|-
 
|-
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| 00:44
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|00:44
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|* '''Jmol version''' '''12.2.2'''
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|'''Jmol version''' '''12.2.2'''
  
 
|-
 
|-
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| 00:47
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|00:47
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|* '''Java''' version '''7'''.  
+
|'''Java''' version '''7'''.  
  
 
|-
 
|-
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| 00:51
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|00:51
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| Display on '''Jmol''' '''panel '''can be modified using:  
+
|Display on '''Jmol''' '''panel '''can be modified using:  
  
 
|-
 
|-
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| 00:55
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|00:55
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|* Options in Menu bar  
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|Options in Menu bar  
  
 
|-
 
|-
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| 00:57
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|00:57
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|* Options in the Pop-up-menu or   
+
|Options in the Pop-up-menu or   
  
 
|-
 
|-
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| 01:00
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|01:00
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|* by '''Scripting commands '''on the script '''console'''.
+
|by '''Scripting commands '''on the script '''console'''.
  
 
|-
 
|-
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| 01:04
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|01:04
 
|We had learnt to modify display using menu bar and pop-up-menu in earlier tutorials.
 
|We had learnt to modify display using menu bar and pop-up-menu in earlier tutorials.
  
 
|-
 
|-
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| 01:13
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|01:13
 
|In this tutorial, we will learn to use '''script commands.'''
 
|In this tutorial, we will learn to use '''script commands.'''
  
 
|-
 
|-
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| 01:18
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|01:18
 
|A set of commands is called a '''script command'''.
 
|A set of commands is called a '''script command'''.
  
 
|-
 
|-
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| 01:22
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|01:22
 
|'''Script commands''' control the display of a '''model''' on '''panel'''.
 
|'''Script commands''' control the display of a '''model''' on '''panel'''.
  
 
|-
 
|-
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| 01:27
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|01:27
 
|'''Jmol''' uses a command language, based on '''RasMol''' program.  
 
|'''Jmol''' uses a command language, based on '''RasMol''' program.  
  
 
|-
 
|-
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| 01:32
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|01:32
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| Writing such commands is called '''scripting.'''
+
|Writing such commands is called '''scripting.'''
  
 
|-
 
|-
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| 01:36
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|01:36
 
|Documentation of Jmol's scripting language and list of commands is available at this link:
 
|Documentation of Jmol's scripting language and list of commands is available at this link:
 
http://chemapps.stolaf.edu/jmol/docs/  
 
http://chemapps.stolaf.edu/jmol/docs/  
  
 
|-
 
|-
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| 01:44
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|01:44
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| Now, how to use''' script commands'''?
+
|Now, how to use''' script commands'''?
  
 
|-
 
|-
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| 01:47
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|01:47
 
|'''Script commands''' are typed on the “'''Script console'''” window.
 
|'''Script commands''' are typed on the “'''Script console'''” window.
  
 
|-
 
|-
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| 01:53
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|01:53
 
|'''Script console''' is the '''command line interface '''of '''Jmol'''.
 
|'''Script console''' is the '''command line interface '''of '''Jmol'''.
  
 
|-
 
|-
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| 01:58
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|01:58
 
|It is available on the menu bar, under '''File '''and '''Console '''option.
 
|It is available on the menu bar, under '''File '''and '''Console '''option.
  
 
|-
 
|-
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| 02:03
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|02:03
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| This is '''Jmol Application''' window with a model of '''propane '''on screen.
+
|This is '''Jmol Application''' window with a model of '''propane '''on screen.
  
 
|-
 
|-
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| 02:08
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|02:08
 
|Let us now learn to use '''Script console '''to change the display.
 
|Let us now learn to use '''Script console '''to change the display.
  
 
|-
 
|-
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| 02:12
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|02:12
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| To open a '''Script console''' window, click on '''File''' menu in the menu bar.
+
|To open a '''Script console''' window, click on '''File''' menu in the menu bar.
  
 
|-
 
|-
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| 02:19
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|02:19
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| In the drop-down, scroll down and click on '''Console.'''
+
|In the drop-down, scroll down and click on '''Console.'''
  
 
|-
 
|-
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| 02:24
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|02:24
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| '''Jmol script console''' window opens on the screen.
+
|'''Jmol script console''' window opens on the screen.
  
 
|-
 
|-
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| 02:29
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|02:29
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| '''Script console''' window has a text area to type the commands.  
+
|'''Script console''' window has a text area to type the commands.  
  
 
|-
 
|-
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| 02:34
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|02:34
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| At the bottom of the window, there is a button to open the '''Script editor''' window.  
+
|At the bottom of the window, there is a button to open the '''Script editor''' window.  
  
 
|-
 
|-
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| 02:40
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|02:40
 
|Other buttons, namely, '''Variables, Clear, History '''and '''State '''are also present on this window.
 
|Other buttons, namely, '''Variables, Clear, History '''and '''State '''are also present on this window.
  
 
|-
 
|-
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| 02:49
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|02:49
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| Click on the '''Help''' button to open a page showing a list of available '''script commands.'''
+
|Click on the '''Help''' button to open a page showing a list of available '''script commands.'''
  
 
|-
 
|-
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| 02:57
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|02:57
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| Click on '''OK''' button to close this window.
+
|Click on '''OK''' button to close this window.
  
 
|-
 
|-
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| 03:01
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|03:01
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| Let us now try to write a few simple script commands.  
+
|Let us now try to write a few simple script commands.  
  
 
|-
 
|-
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| 03:05
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|03:05
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| How to write these commands?
+
|How to write these commands?
  
 
|-
 
|-
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| 03:08
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|03:08
 
|Type the command after the $ (dollar)'''prompt''', on the '''Script console''' window.
 
|Type the command after the $ (dollar)'''prompt''', on the '''Script console''' window.
  
 
|-
 
|-
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| 03:13
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|03:13
 
|'''Script commands '''start with a '''command word''',
 
|'''Script commands '''start with a '''command word''',
  
 
|-
 
|-
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| 03:17
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|03:17
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| continues with a set of '''parameter'''s separated by spaces
+
|continues with a set of '''parameter'''s separated by spaces
  
 
|-
 
|-
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| 03:22
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|03:22
 
|and is terminated by the end of line character or '''semicolon'''.  
 
|and is terminated by the end of line character or '''semicolon'''.  
  
 
|-
 
|-
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| 03:27
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|03:27
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| The command line will appear red, until you have completed typing the '''command'''.
+
|The command line will appear red, until you have completed typing the '''command'''.
  
 
|-
 
|-
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| 03:33
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|03:33
 
|Press '''Enter''' key on the keyboard to activate the command.
 
|Press '''Enter''' key on the keyboard to activate the command.
  
 
|-
 
|-
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| 03:37
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|03:37
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| I am using '''Kmag screen magnifier''' to magnify the '''console'''.
+
|I am using '''Kmag screen magnifier''' to magnify the '''console'''.
  
 
|-
 
|-
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| 03:44
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|03:44
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| For example, to change the color of all the '''carbons''' in '''propane''' to orange- place the cursor on the '''Script Console''' window.
+
|For example, to change the color of all the '''carbons''' in '''propane''' to orange- place the cursor on the '''Script Console''' window.
  
 
|-
 
|-
−
| 03:53
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|03:53
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| At the '''dollar prompt, '''type: ''' select carbon semicolon color atoms orange'''
+
|At the '''dollar prompt, '''type: ''' select carbon semicolon color atoms orange'''
  
 
|-
 
|-
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| 04:05
+
|04:05
 
|Press '''Enter''' key on the keyboard.
 
|Press '''Enter''' key on the keyboard.
  
 
|-
 
|-
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| 04:08
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|04:08
−
| The '''Propane''' model on the panel, now, has all the '''carbons''' in orange color.  
+
|The '''Propane''' model on the panel, now, has all the '''carbons''' in orange color.  
  
 
|-
 
|-
−
| 04:14
+
|04:14
−
| Now, to change the color of all bonds to blue-  
+
|Now, to change the color of all bonds to blue-  
  
 
|-
 
|-
−
| 04:18
+
|04:18
 
|At the dollar prompt, type:
 
|At the dollar prompt, type:
  
 
|-
 
|-
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| 04:20
+
|04:20
 
|'''select all bonds semicolon color bonds blue'''
 
|'''select all bonds semicolon color bonds blue'''
  
Line 229: Line 225:
  
 
|-
 
|-
−
| 04:29
+
|04:29
−
| Observe that all the bonds in the '''propane''' model are now blue in colour.
+
|Observe that all the bonds in the '''propane''' model are now blue in colour.
  
 
|-
 
|-
−
| 04:35
+
|04:35
−
| Next, let us change the size of bonds.
+
|Next, let us change the size of bonds.
  
 
|-
 
|-
−
| 04:39
+
|04:39
 
|At the dollar prompt, type: '''wireframe 0.05'''
 
|At the dollar prompt, type: '''wireframe 0.05'''
  
 
|-
 
|-
−
| 04:45
+
|04:45
 
|The decimal number is used to specify the radius of the bonds, in '''angstroms'''. Press '''Enter.'''
 
|The decimal number is used to specify the radius of the bonds, in '''angstroms'''. Press '''Enter.'''
  
 
|-
 
|-
−
| 04:53
+
|04:53
 
|Note the change in the size of the bonds, in the '''Propane''' model.
 
|Note the change in the size of the bonds, in the '''Propane''' model.
  
 
|-
 
|-
−
| 04:58
+
|04:58
−
| Similarly, to increase the size of the bonds, at the '''prompt''', type: '''wireframe 0.1'''
+
|Similarly, to increase the size of the bonds, at the '''prompt''', type: '''wireframe 0.1'''
  
 
|-
 
|-
−
| 05:07
+
|05:07
 
|Once again, note the change in the size of the bonds.
 
|Once again, note the change in the size of the bonds.
  
 
|-
 
|-
−
| 05:12
+
|05:12
−
| To change the size of the atoms, we will use the command '''spacefill''' followed by a decimal number.
+
|To change the size of the atoms, we will use the command '''spacefill''' followed by a decimal number.
  
 
|-
 
|-
−
| 05:20
+
|05:20
 
|At the dollar prompt, type: '''spacefill 0.2'''.
 
|At the dollar prompt, type: '''spacefill 0.2'''.
  
 
|-
 
|-
−
| 05:26
+
|05:26
 
|The decimal number represents the radius of the atom in '''angstroms.'''
 
|The decimal number represents the radius of the atom in '''angstroms.'''
  
 
|-
 
|-
−
| 05:30
+
|05:30
 
|Press''' Enter.'''  
 
|Press''' Enter.'''  
  
 
|-
 
|-
−
| 05:33
+
|05:33
−
| Observe the size of the atoms in the '''propane''' molecule decrease in size.
+
|Observe the size of the atoms in the '''propane''' molecule decrease in size.
  
 
|-
 
|-
−
| 05:39
+
|05:39
−
| Similarly, to increase the size of the atoms, type:
+
|Similarly, to increase the size of the atoms, type:
  
 
|-
 
|-
−
| 05:43
+
|05:43
 
|'''spacefill 0.5'''
 
|'''spacefill 0.5'''
  
 
|-
 
|-
−
| 05:46
+
|05:46
 
|Press '''Enter'''.
 
|Press '''Enter'''.
  
 
|-
 
|-
−
| 05:48
+
|05:48
−
| You can see the change in size of the atoms.
+
|You can see the change in size of the atoms.
  
 
|-
 
|-
−
| 05:51
+
|05:51
−
| Alternately, we can also use command '''cpk''' followed by percentage or decimal number.
+
|Alternately, we can also use command '''cpk''' followed by percentage or decimal number.
  
 
|-
 
|-
−
| 05:59
+
|05:59
 
|The percentage represents the '''vanderwaals radius''' of the atom.
 
|The percentage represents the '''vanderwaals radius''' of the atom.
  
 
|-
 
|-
−
| 06:04
+
|06:04
−
| For example, type: '''cpk 20% '''and press '''Enter'''.
+
|For example, type: '''cpk 20% '''and press '''Enter'''.
  
 
|-
 
|-
−
| 06:11
+
|06:11
 
|Note the change in the size of the atoms.
 
|Note the change in the size of the atoms.
  
 
|-
 
|-
−
| 06:15
+
|06:15
−
| It is possible to write commands, to display lines of text on the '''Jmol panel.'''
+
|It is possible to write commands, to display lines of text on the '''Jmol panel.'''
  
 
|-
 
|-
−
| 06:22
+
|06:22
 
|The command line for the text starts with ''''set echo'.'''
 
|The command line for the text starts with ''''set echo'.'''
  
 
|-
 
|-
−
| 06:27
+
|06:27
 
|It is followed by the position of the text on the screen.
 
|It is followed by the position of the text on the screen.
  
 
|-
 
|-
−
| 06:31
+
|06:31
−
| For example, we will display the name of the molecule as ''''Propane'''' at the top center of the '''panel'''.
+
|For example, we will display the name of the molecule as ''''Propane'''' at the top center of the '''panel'''.
  
 
|-
 
|-
−
| 06:39
+
|06:39
 
|So, type: '''set echo top center semicolon echo Propane'''
 
|So, type: '''set echo top center semicolon echo Propane'''
 
and press '''Enter'''.
 
and press '''Enter'''.
  
 
|-
 
|-
−
| 06:48
+
|06:48
−
| We can see the text "Propane", displayed at the  top center of the panel.
+
|We can see the text "Propane", displayed at the  top center of the panel.
  
 
|-
 
|-
−
| 06:54
+
|06:54
−
| We can also display other lines of text on the panel.
+
|We can also display other lines of text on the panel.
  
 
|-
 
|-
−
| 06:58
+
|06:58
 
|For example, I want some text in the bottom left corner of the panel.
 
|For example, I want some text in the bottom left corner of the panel.
  
 
|-
 
|-
−
| 07:04
+
|07:04
−
| At the dollar prompt,
+
|At the dollar prompt,
  
 
|-
 
|-
−
| 07:06
+
|07:06
 
|type: '''set echo bottom left semicolon echo This is a model of Propane'''.
 
|type: '''set echo bottom left semicolon echo This is a model of Propane'''.
  
 
|-
 
|-
−
| 07:15
+
|07:15
 
|Press '''Enter.'''
 
|Press '''Enter.'''
  
 
|-
 
|-
 
|07:17
 
|07:17
−
| We can see the text line at the bottom left corner of the panel.
+
|We can see the text line at the bottom left corner of the panel.
  
 
|-
 
|-
−
| 07:22
+
|07:22
−
| It is also possible to change the '''color, size''' and '''font''' of the displayed text.  
+
|It is also possible to change the '''color, size''' and '''font''' of the displayed text.  
  
 
|-
 
|-
−
| 07:29
+
|07:29
−
| For example, I want the text to be in '''Arial Italic '''font.  
+
|For example, I want the text to be in '''Arial Italic '''font.  
  
 
|-
 
|-
−
| 07:34
+
|07:34
 
|At the dollar prompt ($), type: '''font echo 20 Arial italic'''
 
|At the dollar prompt ($), type: '''font echo 20 Arial italic'''
  
 
|-
 
|-
 
|07:42
 
|07:42
−
|Press '''Enter'''.
+
|Press '''Enter''',This will convert the text to''' 'Arial Italic' '''font.
  
 
|-
 
|-
−
| 07:43
+
|07:48
−
|This will convert the text to''' 'Arial Italic' '''font.
+
|To change the color of the text, we will use '''color echo''' followed by name of the colour.
  
 
|-
 
|-
−
| 07:48
+
|07:55
−
| To change the color of the text, we will use '''color echo''' followed by name of the colour.
+
−
 
+
−
|-
+
−
| 07:55
+
 
|So, type: '''"color echo yellow"''' and press '''Enter.'''
 
|So, type: '''"color echo yellow"''' and press '''Enter.'''
  
 
|-
 
|-
−
| 08:01
+
|08:01
 
|Note the change in font colour.
 
|Note the change in font colour.
  
 
|-
 
|-
−
| 08:05
+
|08:05
−
| Likewise, you can explore many more '''command'''s and observe the changes.
+
|Likewise, you can explore many more '''command'''s and observe the changes.
  
 
|-
 
|-
−
| 08:11
+
|08:11
−
| Let's Summarize:
+
|Let's Summarize:
  
 
|-
 
|-
−
| 08:13
+
|08:13
 
|In this tutorial, we have learned about:
 
|In this tutorial, we have learned about:
  
 
|-
 
|-
−
| 08:15
+
|08:15
−
|* '''Script Commands '''and  
+
|'''Script Commands '''and  
−
 
+
−
|-
+
−
| 08:17
+
−
|* '''Script Console. '''
+
  
 
|-
 
|-
−
| 08:18
+
|08:17
−
|We also learned to:  
+
|'''Script Console''',We also learned to:  
  
 
|-
 
|-
−
| 08:19
+
|08:19
−
|* Change the display properties of the model by using '''script commands''' and
+
|Change the display properties of the model by using '''script commands''' and
  
 
|-
 
|-
−
| 08:24
+
|08:24
−
|* Display lines of text on the '''panel.'''
+
|Display lines of text on the '''panel.'''
  
 
|-
 
|-
−
| 08:28
+
|08:28
−
| As an assignment-
+
|As an assignment-
  
 
|-
 
|-
−
| 08:30
+
|08:30
 
|Create a model of '''3-methyl-pentane.'''
 
|Create a model of '''3-methyl-pentane.'''
  
 
|-
 
|-
−
| 08:33
+
|08:33
 
|Use script commands to do the following.
 
|Use script commands to do the following.
  
 
|-
 
|-
−
| 08:36
+
|08:36
−
| Change the color of all the '''hydrogens''' to blue.
+
|Change the color of all the '''hydrogens''' to blue.
  
 
|-
 
|-
−
| 08:40
+
|08:40
−
| Change the color of all the bonds to '''red'''
+
|Change the color of all the bonds to '''red'''
  
 
|-
 
|-
−
| 08:43
+
|08:43
−
| and set the molecule to '''spin'''.
+
|and set the molecule to '''spin'''.
  
 
|-
 
|-
 
|08:46  
 
|08:46  
−
| Watch the video available at this URL:
+
|Watch the video available at this URL:
 
http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
 
http://spoken-tutorial.org/What_is_a_Spoken_Tutorial
  
 
|-
 
|-
−
| 08:49
+
|08:49
 
|It summarizes the '''Spoken Tutorial''' project.
 
|It summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
−
| 08:52
+
|08:52
 
|If you do not have good bandwidth, you can download and watch it.  
 
|If you do not have good bandwidth, you can download and watch it.  
  
 
|-
 
|-
 
|08:57
 
|08:57
−
| The Spoken Tutorial Project team:  
+
|The Spoken Tutorial Project team:  
  
 
|-
 
|-
−
| 08:59
+
|08:59
−
|* Conducts workshops using spoken tutorials.
+
|Conducts workshops using spoken tutorials.
  
 
|-
 
|-
−
| 09:02
+
|09:02
 
|Gives certificates to those who pass an on-line test.  
 
|Gives certificates to those who pass an on-line test.  
  
 
|-
 
|-
−
| 09:06
+
|09:06
 
|For more details, please write to: '''contact@spoken-tutorial.org'''   
 
|For more details, please write to: '''contact@spoken-tutorial.org'''   
  
 
|-
 
|-
−
| 09:13
+
|09:13
−
| '''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.  
  
 
|-
 
|-
−
| 09:17
+
|09:17
 
|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.
  
 
|-
 
|-
−
| 09:24
+
|09:24
 
|More information on this mission is available at this link:
 
|More information on this mission is available at this link:
 
http://spoken-tutorial.org/NMEICT-Intro   
 
http://spoken-tutorial.org/NMEICT-Intro   
  
 
|-
 
|-
−
| 09:30
+
|09:30
−
| This is Snehalatha from '''IIT Bombay''', signing off.  
+
|This is Snehalatha from '''IIT Bombay''', signing off.  
 
Thank you for joining.  
 
Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 17:18, 28 March 2017

Time Narration
00:01 Welcome to this tutorial on Script console and script commands in Jmol Application.
00:08 In this tutorial, we will learn:
00:11 About script commands
00:13 How to use script console window
00:16 Change display of the model by using script commands
00:21 Display lines of text on the panel.
00:24 To follow this tutorial,
00:26 you should know how to,create and edit molecular models in Jmol Application.
00:32 If not, watch the relevant tutorials available on our website.
00:37 To record this tutorial, I am using:
00:39 Ubuntu OS version 12.04
00:44 Jmol version 12.2.2
00:47 Java version 7.
00:51 Display on Jmol panel can be modified using:
00:55 Options in Menu bar
00:57 Options in the Pop-up-menu or
01:00 by Scripting commands on the script console.
01:04 We had learnt to modify display using menu bar and pop-up-menu in earlier tutorials.
01:13 In this tutorial, we will learn to use script commands.
01:18 A set of commands is called a script command.
01:22 Script commands control the display of a model on panel.
01:27 Jmol uses a command language, based on RasMol program.
01:32 Writing such commands is called scripting.
01:36 Documentation of Jmol's scripting language and list of commands is available at this link:

http://chemapps.stolaf.edu/jmol/docs/

01:44 Now, how to use script commands?
01:47 Script commands are typed on the “Script console” window.
01:53 Script console is the command line interface of Jmol.
01:58 It is available on the menu bar, under File and Console option.
02:03 This is Jmol Application window with a model of propane on screen.
02:08 Let us now learn to use Script console to change the display.
02:12 To open a Script console window, click on File menu in the menu bar.
02:19 In the drop-down, scroll down and click on Console.
02:24 Jmol script console window opens on the screen.
02:29 Script console window has a text area to type the commands.
02:34 At the bottom of the window, there is a button to open the Script editor window.
02:40 Other buttons, namely, Variables, Clear, History and State are also present on this window.
02:49 Click on the Help button to open a page showing a list of available script commands.
02:57 Click on OK button to close this window.
03:01 Let us now try to write a few simple script commands.
03:05 How to write these commands?
03:08 Type the command after the $ (dollar)prompt, on the Script console window.
03:13 Script commands start with a command word,
03:17 continues with a set of parameters separated by spaces
03:22 and is terminated by the end of line character or semicolon.
03:27 The command line will appear red, until you have completed typing the command.
03:33 Press Enter key on the keyboard to activate the command.
03:37 I am using Kmag screen magnifier to magnify the console.
03:44 For example, to change the color of all the carbons in propane to orange- place the cursor on the Script Console window.
03:53 At the dollar prompt, type: select carbon semicolon color atoms orange
04:05 Press Enter key on the keyboard.
04:08 The Propane model on the panel, now, has all the carbons in orange color.
04:14 Now, to change the color of all bonds to blue-
04:18 At the dollar prompt, type:
04:20 select all bonds semicolon color bonds blue
04:26 press Enter.
04:29 Observe that all the bonds in the propane model are now blue in colour.
04:35 Next, let us change the size of bonds.
04:39 At the dollar prompt, type: wireframe 0.05
04:45 The decimal number is used to specify the radius of the bonds, in angstroms. Press Enter.
04:53 Note the change in the size of the bonds, in the Propane model.
04:58 Similarly, to increase the size of the bonds, at the prompt, type: wireframe 0.1
05:07 Once again, note the change in the size of the bonds.
05:12 To change the size of the atoms, we will use the command spacefill followed by a decimal number.
05:20 At the dollar prompt, type: spacefill 0.2.
05:26 The decimal number represents the radius of the atom in angstroms.
05:30 Press Enter.
05:33 Observe the size of the atoms in the propane molecule decrease in size.
05:39 Similarly, to increase the size of the atoms, type:
05:43 spacefill 0.5
05:46 Press Enter.
05:48 You can see the change in size of the atoms.
05:51 Alternately, we can also use command cpk followed by percentage or decimal number.
05:59 The percentage represents the vanderwaals radius of the atom.
06:04 For example, type: cpk 20% and press Enter.
06:11 Note the change in the size of the atoms.
06:15 It is possible to write commands, to display lines of text on the Jmol panel.
06:22 The command line for the text starts with 'set echo'.
06:27 It is followed by the position of the text on the screen.
06:31 For example, we will display the name of the molecule as 'Propane' at the top center of the panel.
06:39 So, type: set echo top center semicolon echo Propane

and press Enter.

06:48 We can see the text "Propane", displayed at the top center of the panel.
06:54 We can also display other lines of text on the panel.
06:58 For example, I want some text in the bottom left corner of the panel.
07:04 At the dollar prompt,
07:06 type: set echo bottom left semicolon echo This is a model of Propane.
07:15 Press Enter.
07:17 We can see the text line at the bottom left corner of the panel.
07:22 It is also possible to change the color, size and font of the displayed text.
07:29 For example, I want the text to be in Arial Italic font.
07:34 At the dollar prompt ($), type: font echo 20 Arial italic
07:42 Press Enter,This will convert the text to 'Arial Italic' font.
07:48 To change the color of the text, we will use color echo followed by name of the colour.
07:55 So, type: "color echo yellow" and press Enter.
08:01 Note the change in font colour.
08:05 Likewise, you can explore many more commands and observe the changes.
08:11 Let's Summarize:
08:13 In this tutorial, we have learned about:
08:15 Script Commands and
08:17 Script Console,We also learned to:
08:19 Change the display properties of the model by using script commands and
08:24 Display lines of text on the panel.
08:28 As an assignment-
08:30 Create a model of 3-methyl-pentane.
08:33 Use script commands to do the following.
08:36 Change the color of all the hydrogens to blue.
08:40 Change the color of all the bonds to red
08:43 and set the molecule to spin.
08:46 Watch the video available at this URL:

http://spoken-tutorial.org/What_is_a_Spoken_Tutorial

08:49 It summarizes the Spoken Tutorial project.
08:52 If you do not have good bandwidth, you can download and watch it.
08:57 The Spoken Tutorial Project team:
08:59 Conducts workshops using spoken tutorials.
09:02 Gives certificates to those who pass an on-line test.
09:06 For more details, please write to: contact@spoken-tutorial.org
09:13 Spoken Tutorial project is a part of the Talk to a Teacher project.
09:17 It is supported by the National Mission on Education through ICT, MHRD, Government of India.
09:24 More information on this mission is available at this link:

http://spoken-tutorial.org/NMEICT-Intro

09:30 This is Snehalatha from IIT Bombay, signing off.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14

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