Jmol-Application/C4/Animation-using-Script-Commands/English-timed

Time	Narration
00:01	Welcome to this tutorial on Animation using Script Commands.
00:06	In this tutorial, we will learn to show animations using Jmol script commands.
00:12	For demonstration, we will use models of ethane and hemoglobin as examples.
00:19	Jmol script commands with the following keywords will be used for animations.
00:24	move, delay, slab, loop and capture.
00:30	To follow this tutorial, you should have knowledge of high school chemistry and familiar with operations from Jmol window.
00:39	If not, for relevant tutorials, please visit our website.
00:44	To record this tutorial, I am using Ubuntu OS version 14.10,
00:51	Jmol version 14.1.11 and Java version 7.
00:58	This slide shows the function of each animation command in detail.
01:03	move command allows you to rotate, zoom and translate a model within a specified period of time.
01:11	delay command is used to pause a script for the specified number of seconds.
01:17	slab command is used to control the percentage of the molecule to be displayed on panel.
01:23	loop command causes the script to restart at the beginning, with an optional time delay.
01:30	capture command captures animations as animated GIF files.
01:36	For more details on Jmol script command, visit the web page for Jmol interactive script documentation.
01:44	Let us open the Jmol window and demonstrate an animation using move command.
01:50	I will begin with a simple move command using ethane as an example.
01:55	Create a model of ethane using modelkit menu.
01:59	Click on the modelkit icon, a model of methane appears on the screen.
02:06	Click on the hydrogen. Now we have a model of ethane on screen.
02:13	Open the console using File menu.
02:17	At the prompt, type the following command.
02:21	The command line starts with the word "move"
02:24	followed by the numbers that quantify a set of animation parameters.
02:29	More information about move command: There are nine parameters in the move command.
02:36	The first three parameters are rotations around X, Y and Z axes. 4th is the zoom modifier, expressed in positive or negative numbers,
02:48	positive for zoom in and negative for zoom out.
02:52	The next three parameters deal with translation along the three axes.
02:57	8th is the slab parameter. Slab slices the molecule.
03:03	It removes atoms to a specified depth so that interior features may be easily observed.
03:10	Parameter 9 is the amount of time, in seconds, taken in performing the move command.
03:17	Back to the Jmol panel.
03:20	Press Enter and observe the panel.
03:25	We can create more interesting animation by adding more commands to the existing ones.
03:31	Press up-arrow key on the key board to get the previous command.
03:36	Type: delay space 2 after the semicolon.
03:41	Here, the delay command pauses the script for 2 seconds, before executing the next command.
03:48	Then type another move command after this delay command.
03:52	Don't forget to add semicolon at the end of each keyword command. Press Enter. Observe the panel.
04:06	We can also change the color of the atoms during this animation.
04:10	Again, press up-arrow key to get the previous command.
04:15	Edit the command as I have shown here, on the console.
04:19	Use select keywords to change the color of the hydrogens and carbons. Press Enter.
04:27	Again observe the panel.
04:34	Add a "slab" command to make certain parts of the molecule to disappear and appear.
04:41	Press up-arrow key again and edit the previous command as shown on the console.
04:47	Type: "slab on" after the select command.
04:51	Type: "slab off" at the end of the command.
04:55	Press Enter and observe the panel.
05:01	You can see parts of the molecule disappear and appear again.
05:06	You can save this animation as a GIF file, using capture keyword.
05:11	Press up-arrow key to get the previous command.
05:15	Type the "capture" command and specify the file name and path at the beginning of the command.
05:21	You can type the name of your home folder to save the GIF file.
05:26	I am saving this animation as file “sneha”, on the desktop. Press Enter.
05:36	Now the animation will be saved as GIF file on my desktop.
05:41	Navigate to the location of the GIF file.
05:44	Open the saved GIF file with Image Viewer software.
05:50	Back to the Jmol panel.
05:54	Similarly, open a pdb file of any macromolecule; for example- oxygenated hemoglobin with a pdb code "2DN1".
06:06	Download the structure directly from pdb database using File menu.
06:11	Type the pdb code in the text-box, "2DN1". Press OK.
06:19	A model of hemoglobin is displayed on the panel.
06:23	Type the following command in the Console.
06:26	We have used select keyword command to change the color of different units of the protein.
06:32	We have also used move command.
06:35	This command will display protein in red cartoons.
06:40	The Haem part in yellow spacefill display and cut away 50% of the molecule.
06:48	Rotate 360º on X-axis in 4 seconds and restore all atoms.
06:56	Press Enter and observe the panel.
07:07	Let us now use the loop command to repeat all the above steps.
07:13	Press up-arrow key to get the same command. Type "loop 2" at the end of the command.
07:20	"loop 2" indicates the previous script commands will be repeated after a 2 second delay. Press Enter.
07:34	You can be creative and type many more such commands to animate.
07:39	Now, let's summarize. In this tutorial, we have learnt to
07:44	create animation of ethane and haemoglobin using script commands such as move, delay.
07:54	We have also made use of loop and slab commands.
07:58	Saved the animations as a GIF file using capture command.
08:03	For the assignment- Take a molecule of your choice and create animation using move and delay commands.
08:11	Change display, color and size of the bonds to create animation.
08:17	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
08:25	The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test.
08:32	For more details, please write to us.
08:36	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
08:43	More information on this mission is available at the link shown.
08:48	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14