Jmol-Application/C4/Animation-using-Script-Commands/English-timed
From Script | Spoken-Tutorial
| 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.4is 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. |
