Difference between revisions of "Jmol-Application/C4/Animation-using-Script-Commands/English-timed"
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| − | + | |'''Time''' | |
| − | + | |'''Narration''' | |
|- | |- | ||
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|- | |- | ||
| − | | 00:06 | + | |00:06 |
|In this tutorial, we will learn to show '''animation'''s using '''Jmol script command'''s. | |In this tutorial, we will learn to show '''animation'''s using '''Jmol script command'''s. | ||
|- | |- | ||
| − | | 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. | ||
|- | |- | ||
| − | | 00:19 | + | |00:19 |
| − | |'''Jmol script command'''s with the following '''keyword'''s will be used for | + | |'''Jmol script command'''s with the following '''keyword'''s will be used for '''animation'''s. |
|- | |- | ||
| − | | 00:24 | + | |00:24 |
|'''move, delay, slab, loop '''and''' capture'''. | |'''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'''. | |To follow this tutorial, you should have knowledge of high school chemistry and familiar with operations from '''Jmol window'''. | ||
|- | |- | ||
| − | | 00:39 | + | |00:39 |
|If not, for relevant tutorials, please visit our website. | |If not, for relevant tutorials, please visit our website. | ||
|- | |- | ||
| − | | 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, |
|- | |- | ||
| − | | 00:51 | + | |00:51 |
| − | |'''Jmol''' version | + | |'''Jmol''' version 14.1.11 and '''Java''' version 7. |
|- | |- | ||
| − | | 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. | ||
|- | |- | ||
| − | | 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. | ||
| Line 53: | Line 52: | ||
|- | |- | ||
| − | | 01:17 | + | |01:17 |
|'''slab '''command is used to control the percentage of the molecule to be displayed on panel. | |'''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 | + | |'''loop '''command causes the script to restart at the beginning with an optional time delay. |
| − | time delay. | + | |
|- | |- | ||
| − | | 01:30 | + | |01:30 |
|'''capture '''command captures animations as animated '''GIF''' files. | |'''capture '''command captures animations as animated '''GIF''' files. | ||
|- | |- | ||
| − | | 01:36 | + | |01:36 |
|For more details on '''Jmol''' script command, visit the web page for '''Jmol interactive script documentation'''. | |For more details on '''Jmol''' script command, visit the web page for '''Jmol interactive script documentation'''. | ||
|- | |- | ||
| − | | | + | |01:44 |
| − | |Let us open the | + | |Let us open the Jmol window and demonstrate an animation using '''move''' command. |
|- | |- | ||
| − | | | + | |01:50 |
| − | |I will begin with a simple '''move''' command using | + | |I will begin with a simple '''move''' command using ethane as an example. |
|- | |- | ||
| − | | 01:55 | + | |01:55 |
|Create a model of '''ethane''' using '''modelkit''' menu. | |Create a model of '''ethane''' using '''modelkit''' menu. | ||
|- | |- | ||
| − | | | + | |01:59 |
|Click on the '''modelkit''' icon, a model of '''methane''' appears on the '''screen'''. | |Click on the '''modelkit''' icon, a model of '''methane''' appears on the '''screen'''. | ||
|- | |- | ||
| − | | 02:06 | + | |02:06 |
|Click on the '''hydrogen'''. Now we have a model of '''ethane''' on screen. | |Click on the '''hydrogen'''. Now we have a model of '''ethane''' on screen. | ||
|- | |- | ||
| − | | | + | |02:13 |
|Open the '''console''' using '''File''' menu. | |Open the '''console''' using '''File''' menu. | ||
|- | |- | ||
| − | | | + | |02:17 |
|At the prompt, type the following command. | |At the prompt, type the following command. | ||
|- | |- | ||
| − | | 02:21 | + | |02:21 |
|The '''command line''' starts with the word "move" | |The '''command line''' starts with the word "move" | ||
|- | |- | ||
| − | | 02:24 | + | |02:24 |
|followed by the numbers that quantify a set of '''animation parameter'''s. | |followed by the numbers that quantify a set of '''animation parameter'''s. | ||
|- | |- | ||
| − | | 02:29 | + | |02:29 |
|More information about '''move''' command: There are nine parameters in the '''move''' command. | |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. | + | |The first three parameters are rotations around X, Y and Z axes.4is the '''zoom modifier''', expressed in positive or negative numbers, |
| − | + | ||
| − | + | ||
|- | |- | ||
| − | | 02:48 | + | |02:48 |
|positive for '''zoom in''' and negative for '''zoom out'''. | |positive for '''zoom in''' and negative for '''zoom out'''. | ||
|- | |- | ||
| − | | 02:52 | + | |02:52 |
|The next three parameters deal with '''translation''' along the three axes. | |The next three parameters deal with '''translation''' along the three axes. | ||
|- | |- | ||
| − | | 02:57 | + | |02:57 |
|8th is the '''slab''' parameter. Slab '''slice'''s the molecule. | |8th is the '''slab''' parameter. Slab '''slice'''s the molecule. | ||
|- | |- | ||
| − | | 03:03 | + | |03:03 |
|It removes atoms to a specified depth so that interior features may be easily observed. | |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 '''second'''s, taken in performing the '''move''' command. | |Parameter 9 is the amount of time, in '''second'''s, taken in performing the '''move''' command. | ||
|- | |- | ||
| − | | 03:17 | + | |03:17 |
|Back to the '''Jmol''' panel. | |Back to the '''Jmol''' panel. | ||
|- | |- | ||
| − | | 03:20 | + | |03:20 |
|Press '''Enter''' and observe the panel. | |Press '''Enter''' and observe the panel. | ||
|- | |- | ||
| − | | 03:25 | + | |03:25 |
|We can create more interesting animation by adding more commands to the existing ones. | |We can create more interesting animation by adding more commands to the existing ones. | ||
|- | |- | ||
| − | | 03:31 | + | |03:31 |
|Press up-arrow key on the key board to get the previous command. | |Press up-arrow key on the key board to get the previous command. | ||
|- | |- | ||
| − | | | + | |03:36 |
|Type: '''delay space 2''' after the semicolon. | |Type: '''delay space 2''' after the semicolon. | ||
|- | |- | ||
| − | | 03:41 | + | |03:41 |
|Here, the '''delay''' command pauses the script for 2 seconds, before executing the next command. | |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. | |Then type another '''move''' command after this '''delay''' command. | ||
|- | |- | ||
| − | | 03:52 | + | |03:52 |
|Don't forget to add semicolon at the end of each '''keyword''' command. Press '''Enter'''. Observe the panel. | |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. | |We can also change the color of the atoms during this animation. | ||
|- | |- | ||
| − | | 04:10 | + | |04:10 |
|Again, press up-arrow key to get the previous command. | |Again, press up-arrow key to get the previous command. | ||
|- | |- | ||
| − | | | + | |04:15 |
|'''Edit''' the command as I have shown here, on the console. | |'''Edit''' the command as I have shown here, on the console. | ||
|- | |- | ||
| − | | 04:19 | + | |04:19 |
|Use '''select''' keywords to change the color of the hydrogens and carbons. Press '''Enter'''. | |Use '''select''' keywords to change the color of the hydrogens and carbons. Press '''Enter'''. | ||
| + | |||
|- | |- | ||
| − | | | + | |04:27 |
|Again observe the panel. | |Again observe the panel. | ||
|- | |- | ||
| − | | 04:34 | + | |04:34 |
|Add a "slab" command to make certain parts of the molecule to disappear and appear. | |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. | |Press up-arrow key again and edit the previous command as shown on the console. | ||
|- | |- | ||
| − | | | + | |04:47 |
|Type: "slab on" after the '''select''' command. | |Type: "slab on" after the '''select''' command. | ||
|- | |- | ||
| − | | 04:51 | + | |04:51 |
|Type: "slab off" at the end of the command. | |Type: "slab off" at the end of the command. | ||
|- | |- | ||
| − | | 04:55 | + | |04:55 |
|Press '''Enter''' and observe the panel. | |Press '''Enter''' and observe the panel. | ||
|- | |- | ||
| − | | 05:01 | + | |05:01 |
|You can see parts of the molecule disappear and appear again. | |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. | |You can save this animation as a '''GIF''' file, using '''capture''' keyword. | ||
|- | |- | ||
| − | | 05:11 | + | |05:11 |
|Press up-arrow key to get the previous command. | |Press up-arrow key to get the previous command. | ||
|- | |- | ||
| − | | 05:15 | + | |05:15 |
| − | |Type the "capture" command and specify the file name and path at the beginning of the command. | + | |Type the "capture" command and specify the file name and '''path''' at the beginning of the command. |
|- | |- | ||
| − | | 05:21 | + | |05:21 |
| − | |You can type the name of your home folder to save the '''GIF''' file. | + | |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'''. | |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. | |Now the animation will be saved as''' GIF''' file on my desktop. | ||
|- | |- | ||
| − | | | + | |05:41 |
|Navigate to the location of the '''GIF''' file. | |Navigate to the location of the '''GIF''' file. | ||
|- | |- | ||
| − | | 05:44 | + | |05:44 |
|Open the saved '''GIF''' file with '''Image Viewer''' software. | |Open the saved '''GIF''' file with '''Image Viewer''' software. | ||
|- | |- | ||
| − | | 05:50 | + | |05:50 |
|Back to the '''Jmol''' panel. | |Back to the '''Jmol''' panel. | ||
|- | |- | ||
| − | | | + | |05:54 |
|Similarly, open a '''pdb''' file of any macromolecule; for example- '''oxygenated hemoglobin''' with a '''pdb code''' "2DN1". | |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. | |Download the structure directly from '''pdb''' database using '''File''' menu. | ||
|- | |- | ||
| − | | 06:11 | + | |06:11 |
|Type the '''pdb code''' in the text-box, "2DN1". Press '''OK'''. | |Type the '''pdb code''' in the text-box, "2DN1". Press '''OK'''. | ||
|- | |- | ||
| − | | 06:19 | + | |06:19 |
|A model of '''hemoglobin''' is displayed on the panel. | |A model of '''hemoglobin''' is displayed on the panel. | ||
|- | |- | ||
| − | | 06:23 | + | |06:23 |
|Type the following command in the '''Console.''' | |Type the following command in the '''Console.''' | ||
|- | |- | ||
| − | | 06:26 | + | |06:26 |
|We have used '''select''' keyword command to change the color of different units of the protein. | |We have used '''select''' keyword command to change the color of different units of the protein. | ||
|- | |- | ||
| − | | 06:32 | + | |06:32 |
|We have also used '''move '''command. | |We have also used '''move '''command. | ||
|- | |- | ||
| − | | | + | |06:35 |
|This command will display protein in red cartoons. | |This command will display protein in red cartoons. | ||
|- | |- | ||
| − | | 06:40 | + | |06:40 |
|The''' Haem''' part in '''yellow spacefill display '''and cut away 50% of the molecule. | |The''' Haem''' part in '''yellow spacefill display '''and cut away 50% of the molecule. | ||
|- | |- | ||
| − | | 06:48 | + | |06:48 |
|Rotate 360º on X-axis in 4 seconds and restore all atoms. | |Rotate 360º on X-axis in 4 seconds and restore all atoms. | ||
|- | |- | ||
| − | | 06:56 | + | |06:56 |
|Press '''Enter''' and observe the panel. | |Press '''Enter''' and observe the panel. | ||
|- | |- | ||
| − | | | + | |07:07 |
|Let us now use the '''loop''' command to repeat all the above steps. | |Let us now use the '''loop''' command to repeat all the above steps. | ||
|- | |- | ||
| − | | 07:13 | + | |07:13 |
|Press up-arrow key to get the same command. Type "loop 2" at the end of the command. | |Press up-arrow key to get the same command. Type "loop 2" at the end of the command. | ||
|- | |- | ||
| − | | 07:20 | + | |07:20 |
| − | |"loop 2" indicates the previous script commands will be repeated after a 2 second delay. | + | |"'''loop 2'''" indicates the previous script commands will be repeated after a 2 second delay.Press '''Enter'''. |
| − | Press '''Enter'''. | + | |
|- | |- | ||
| − | | | + | |07:34 |
|You can be creative and type many more such commands to animate. | |You can be creative and type many more such commands to animate. | ||
|- | |- | ||
| − | | 07:39 | + | |07:39 |
|Now, let's summarize. In this tutorial, we have learnt to | |Now, let's summarize. In this tutorial, we have learnt to | ||
|- | |- | ||
| − | | 07:44 | + | |07:44 |
|create animation of '''ethane''' and '''haemoglobin ''' using script commands such as '''move''', '''delay'''. | |create animation of '''ethane''' and '''haemoglobin ''' using script commands such as '''move''', '''delay'''. | ||
|- | |- | ||
| − | | 07:54 | + | |07:54 |
|We have also made use of''' loop''' and '''slab''' commands. | |We have also made use of''' loop''' and '''slab''' commands. | ||
|- | |- | ||
| − | | 07:58 | + | |07:58 |
|Saved the animations as a '''GIF''' file using '''capture''' command. | |Saved the animations as a '''GIF''' file using '''capture''' command. | ||
|- | |- | ||
| − | | | + | |08:03 |
| − | |For the assignment- | + | |For the assignment-Take a molecule of your choice and create animation using '''move''' and '''delay''' commands.<br/> |
| − | Take a molecule of your choice and create animation using '''move''' and '''delay''' commands.<br/> | + | |
|- | |- | ||
| − | | 08:11 | + | |08:11 |
| − | | Change display, color and size of the bonds to create animation. | + | |Change display, color and size of the bonds to create animation. |
|- | |- | ||
| − | | 08:17 | + | |08:17 |
| − | |The video at the following link summarizes the '''Spoken Tutorial''' project. | + | |The video at the following link summarizes the '''Spoken Tutorial''' project. Please download and watch it. |
| − | Please download and watch it. | + | |
|- | |- | ||
| − | | 08:25 | + | |08:25 |
|The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test. | |The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test. | ||
|- | |- | ||
| − | | 08:32 | + | |08:32 |
|For more details, please write to us. | |For more details, please write to us. | ||
|- | |- | ||
| − | | | + | |08:36 |
|Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. | |Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. | ||
|- | |- | ||
| − | | 08:43 | + | |08:43 |
|More information on this mission is available at the link shown. | |More information on this mission is available at the link shown. | ||
|- | |- | ||
| − | | 08:48 | + | |08:48 |
|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. | |This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining. | ||
| − | |||
|} | |} | ||
Latest revision as of 10:11, 29 March 2017
| 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. |
