Difference between revisions of "Jmol-Application/C2/Script-Console-and-Script-Commands/English-timed"
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| − | |* Change display of model by using '''script commands''' | + | |* Change display of the model by using '''script commands''' |
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| 00:39 | | 00:39 | ||
| − | | * '''Ubuntu '''OS version | + | | * '''Ubuntu '''OS version 12.04 |
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| 00:44 | | 00:44 | ||
| − | |* '''Jmol version''' 12.2.2 | + | |* '''Jmol version''' '''12.2.2''' |
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| 00:47 | | 00:47 | ||
| − | |* '''Java''' version 7. | + | |* '''Java''' version '''7'''. |
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| 01:04 | | 01:04 | ||
| − | |We had learnt to modify display using menu bar and | + | |We had learnt to modify display using menu bar and pop-up-menu in earlier tutorials. |
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| 01:18 | | 01:18 | ||
| − | |A set of commands is called ''' | + | |A set of commands is called a '''script command'''. |
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| 01:36 | | 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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| 03:08 | | 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. |
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| 03:17 | | 03:17 | ||
| − | | continues with a set of | + | | continues with a set of '''parameter'''s separated by spaces |
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| 03:22 | | 03:22 | ||
| − | | | + | |and is terminated by the end of line character or '''semicolon'''. |
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| 03:27 | | 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'''. |
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| 04:08 | | 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. |
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| 04:29 | | 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. |
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| 04:45 | | 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.''' |
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| 04:53 | | 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. |
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| 04:58 | | 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''' |
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| 05:07 | | 05:07 | ||
| − | |Once again, note the change in size of the bonds. | + | |Once again, note the change in the size of the bonds. |
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| 05:12 | | 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. |
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| 05:20 | | 05:20 | ||
| − | |At the dollar prompt, type: '''spacefill 0.2''' | + | |At the dollar prompt, type: '''spacefill 0.2'''. |
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| 05:26 | | 05:26 | ||
| − | |The decimal number represents radius of the atom in '''angstroms.''' | + | |The decimal number represents the radius of the atom in '''angstroms.''' |
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| 05:33 | | 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. |
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| 06:22 | | 06:22 | ||
| − | |The command line for text starts with ''''set echo'.''' | + | |The command line for the text starts with ''''set echo'.''' |
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| 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'''. |
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|07:17 | |07:17 | ||
| − | | We can see the text line at the bottom left corner of the | + | | We can see the text line at the bottom left corner of the panel. |
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| 07:48 | | 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. |
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| 08:36 | | 08:36 | ||
| − | | Change the color of all '''hydrogens''' to blue. | + | | Change the color of all the '''hydrogens''' to blue. |
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| 08:43 | | 08:43 | ||
| − | | and set the molecule to spin. | + | | and set the molecule to '''spin'''. |
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|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 | ||
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| 08:49 | | 08:49 | ||
| − | |It summarizes the Spoken Tutorial project. | + | |It summarizes the '''Spoken Tutorial''' project. |
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| 09:06 | | 09:06 | ||
| − | |For more details, please write to: contact@spoken-tutorial.org | + | |For more details, please write to: '''contact@spoken-tutorial.org''' |
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Revision as of 18:18, 5 June 2016
| 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 |
| 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 | * 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: |
| 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. |
| 07:43 | 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. |
| 08:18 | 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: |
| 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: |
| 09:30 | This is Snehalatha from IIT Bombay, signing off.
Thank you for joining. |
