Difference between revisions of "Jmol-Application/C4/Animation-using-Script-Commands/English-timed"
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| − | |In this tutorial, we will learn to show | + | |In this tutorial, we will learn to show '''animation'''s using '''Jmol script command'''s. |
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| 00:12 | | 00:12 | ||
| − | |For demonstration we will use models of '''ethane''' and''' hemoglobin '''as examples. | + | |For demonstration, we will use models of '''ethane''' and''' hemoglobin '''as examples. |
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| 00:19 | | 00:19 | ||
| − | |'''Jmol''' | + | |'''Jmol script command'''s with the following '''keyword'''s will be used for animations. |
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| 00:24 | | 00:24 | ||
| − | |'''Move, delay, slab, loop '''and''' capture | + | |'''Move, delay, slab, loop '''and''' capture'''. |
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| 00:30 | | 00:30 | ||
| − | |To follow this tutorial you should have knowledge of | + | |To follow this tutorial, you should have knowledge of high school Chemistry and familiar with operations from '''Jmol window'''. |
| − | and familiar with operations from '''Jmol''' | + | |
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| 00:44 | | 00:44 | ||
| − | |To record this tutorial I am using '''Ubuntu OS''' version | + | |To record this tutorial, I am using '''Ubuntu OS''' version '''14.10''' |
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| 00:51 | | 00:51 | ||
| − | |'''Jmol''' version 14.1.11 and '''Java''' version 7 | + | |'''Jmol''' version '''14.1.11''' and '''Java''' version '''7'''. |
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| 00:58 | | 00:58 | ||
| − | |This slide shows the function of each animation command in detail. | + | |This '''slide''' shows the function of each '''animation command''' in detail. |
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| 01:03 | | 01:03 | ||
| − | |'''move''' command allows you to rotate, zoom and translate a model within a specified period of time. | + | |'''move''' command allows you to '''rotate, zoom''' and '''translate''' a '''model''' within a specified period of time. |
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|01:11 | |01:11 | ||
| − | |'''delay '''command is used to pause | + | |'''delay '''command is used to pause a script for the specified number of seconds. |
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| − | | | + | |'''loop '''command causes the script to restart at the beginning, with an optional |
| − | time delay . | + | time delay. |
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| 01:30 | | 01:30 | ||
| − | | | + | |'''capture '''command captures animations as animated '''GIF''' files. |
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| 01:36 | | 01:36 | ||
| − | |For more details on '''Jmol''' script command | + | |For more details on '''Jmol''' script command, visit the web page for '''Jmol interactive script documentation'''. |
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Revision as of 18:03, 11 February 2016
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| 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 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 one. |
| 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 key words 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 key word. |
| 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 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, Lets 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,
|
| 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. |
