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

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	* 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. [1]
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 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 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