Jmol-Application/C2/Script-Console-and-Script-Commands/English-timed
From Script | Spoken-Tutorial
Revision as of 12:16, 20 October 2014 by PoojaMoolya (Talk | contribs)
| 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. |
| 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_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. |
