Jmol-Application/C2/Script-Console-and-Script-Commands/English-timed - Revision history

PoojaMoolya at 11:48, 28 March 2017

2017-03-28T11:48:24Z

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Sandhya.np14 at 12:48, 5 June 2016

2016-06-05T12:48:30Z

Sandhya.np14 at 12:35, 30 March 2016

2016-03-30T12:35:47Z

Sandhya.np14 at 04:48, 14 September 2015

2015-09-14T04:48:23Z

Sandhya.np14 at 04:46, 14 September 2015

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PoojaMoolya at 06:46, 20 October 2014

2014-10-20T06:46:27Z

Pratik kamble: moved Jmol Application/C2/Script-Console-and-Script-Commands/English-timed to Jmol-Application/C2/Script-Console-and-Script-Commands/English-timed: _ changed to -

2014-08-20T05:01:16Z

moved Jmol Application/C2/Script-Console-and-Script-Commands/English-timed to Jmol-Application/C2/Script-Console-and-Script-Commands/English-timed: _ changed to -

Pratik kamble: Created page with '{| border=1 |'''Time''' |'''Narration''' |- | 00:01 | Welcome to this tutorial on '''Script console and script commands '''in '''Jmol Application'''. |- | 00:08 |In this tutori…'

2014-08-14T12:04:58Z

Created page with '{| border=1 |'''Time''' |'''Narration''' |- | 00:01 | Welcome to this tutorial on '''Script console and script commands '''in '''Jmol Application'''. |- | 00:08 |In this tutori…'

New page

{| border=1
|'''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 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

|-
| 00:27
|* 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
| I am using '''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 '''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/ 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 $ '''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 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 '''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 bonds, in '''angstroms'''. Press '''Enter.'''

|-
| 04:53
|Note the change in size of the bonds in the '''Propane''' model.

|-
| 04:58
| Similarly, to increase the size of bonds, at the '''prompt''', type '''wireframe 0.1'''

|-
| 05:07
|Once again, note the change in size of the bonds.

|-
| 05:12
| To change the size of 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 radius of the atom, in '''angstroms.'''

|-
| 05:30
|Press''' Enter.'''

|-
| 05:33
| Observe the size of 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 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

|-
| 07:43
|This will convert the text to''' 'Arial Italic' '''font.

|-
| 07:48
| To change 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 learnt about:

|-
| 08:15
|* '''Script Commands '''and

|-
| 08:17
|* '''Script Console '''

|-
| 08:18
|We also learnt 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 '''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 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 http://spoken-tutorial.org/NMEICT-Intro] ]

|-
| 09:30
| This is Snehalatha from IIT Bombay signing off.
Thank you for joining.

|}

@@ Line 102: / Line 102: @@
 | 01:36
 |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/
 |-
@@ Line 448: / Line 448: @@
 |08:46
 | 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
 |-

@@ Line 21: / Line 21: @@
 |-
 | 00:16
-|* Change display of model by using '''script commands'''
+|* Change display of the model by using '''script commands'''
 |-
@@ Line 49: / Line 49: @@
 |-
 | 00:39
-| * '''Ubuntu '''OS version. 12.04
+| * '''Ubuntu '''OS version 12.04
 |-
 | 00:44
-|* '''Jmol version''' 12.2.2
+|* '''Jmol version''' '''12.2.2'''
 |-
 | 00:47
-|* '''Java''' version 7.
+|* '''Java''' version '''7'''.
 |-
@@ Line 77: / Line 77: @@
 |-
 | 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.
 |-
@@ Line 85: / Line 85: @@
 |-
 | 01:18
-|A set of commands is called '''Script command'''.
+|A set of commands is called a '''script command'''.
 |-
@@ Line 101: / Line 101: @@
 |-
 | 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/
@@ Line 170: / Line 170: @@
 |-
 | 03:08
-|Type the command after the $ '''prompt''' on the '''Script console''' window.
+|Type the command after the $ (dollar)'''prompt''', on the '''Script console''' window.
 |-
@@ Line 178: / Line 178: @@
 |-
 | 03:17
-| continues with a set of parameters separated by spaces.
+| continues with a set of '''parameter'''s separated by spaces
 |-
 | 03:22
-|And is terminated by the end of line character or '''semicolon'''.
+|and is terminated by the end of line character or '''semicolon'''.
 |-
 | 03:27
-| The command will appear red, until you have completed typing the command.
+| The command line will appear red, until you have completed typing the '''command'''.
 |-
@@ Line 210: / Line 210: @@
 |-
 | 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.
 |-
@@ Line 230: / Line 230: @@
 |-
 | 04:29
-| Observe that all the bonds in '''propane''' model are now blue in colour.
+| Observe that all the bonds in the '''propane''' model are now blue in colour.
 |-
@@ Line 242: / Line 242: @@
 |-
 | 04:45
-|The decimal number is used to specify the radius of bonds, in '''angstroms'''. Press '''Enter.'''
+|The decimal number is used to specify the radius of the bonds, in '''angstroms'''. Press '''Enter.'''
 |-
 | 04:53
-|Note the change in size of the bonds in the '''Propane''' model.
+|Note the change in the size of the bonds, in the '''Propane''' model.
 |-
 | 04:58
-| Similarly, to increase the size of 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
-|Once again, note the change in size of the bonds.
+|Once again, note the change in the size of the bonds.
 |-
 | 05:12
-| To change the size of 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
-|At the dollar prompt, type: '''spacefill 0.2'''
+|At the dollar prompt, type: '''spacefill 0.2'''.
 |-
 | 05:26
-|The decimal number represents radius of the atom in '''angstroms.'''
+|The decimal number represents the radius of the atom in '''angstroms.'''
 |-
@@ Line 274: / Line 274: @@
 |-
 | 05:33
-| Observe the size of atoms in the '''propane''' molecule decrease in size.
+| Observe the size of the atoms in the '''propane''' molecule decrease in size.
 |-
@@ Line 314: / Line 314: @@
 |-
 | 06:22
-|The command line for text starts with ''''set echo'.'''
+|The command line for the text starts with ''''set echo'.'''
 |-
@@ Line 347: / Line 347: @@
 |-
 | 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'''.
 |-
@@ Line 355: / Line 355: @@
 |-
 |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.
 |-
@@ Line 379: / Line 379: @@
 |-
 | 07:48
-| To change color of the text, we will use '''color echo''' followed by name of the colour.
+| To change the color of the text, we will use '''color echo''' followed by name of the colour.
 |-
@@ Line 435: / Line 435: @@
 |-
 | 08:36
-| Change the color of all '''hydrogens''' to blue.
+| Change the color of all the '''hydrogens''' to blue.
 |-
@@ Line 443: / Line 443: @@
 |-
 | 08:43
-| and set the molecule to spin.
+| and set the molecule to '''spin'''.
 |-
 |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
 |-
 | 08:49
-|It summarizes the Spoken Tutorial project.
+|It summarizes the '''Spoken Tutorial''' project.
 |-
@@ Line 472: / Line 472: @@
 |-
 | 09:06
-|For more details, please write to: contact@spoken-tutorial.org
+|For more details, please write to: '''contact@spoken-tutorial.org'''
 |-

@@ Line 266: / Line 266: @@
 |-
 | 05:26
-|The decimal number represents radius of the atom, in '''angstroms.'''
+|The decimal number represents radius of the atom in '''angstroms.'''
 |-
@@ Line 331: / Line 331: @@
 |-
 | 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
-| We can also display other lines of text on the '''panel. '''
+| 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.'''
+|For example, I want some text in the bottom left corner of the panel.
 |-

@@ Line 86: / Line 86: @@
 | 01:18
 |A set of commands is called '''Script command'''.
 |-
 | 01:22
 |'''Script commands''' control the display of a '''model''' on '''panel'''
 |-
@@ Line 100: / Line 98: @@
 | 01:32
 | Writing such commands is called '''scripting.'''
 |-
@@ Line 203: / Line 199: @@
 | 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'''
 |-
@@ Line 355: / Line 348: @@
 | 07:06
 |type '''set echo bottom left semicolon echo This is a model of Propane'''
 |-

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