Difference between revisions of "Jmol-Application/C4/Animation-using-Script-Commands/English-timed"

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{| Border=1
 
{| Border=1
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! <center>Time</center>
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|'''Time'''
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! <center>Narration</center>
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|'''Narration'''
  
 
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|-
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|-
 
|-
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|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.
  
 
|-
 
|-
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| 00:12
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|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
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|00:19
 
|'''Jmol script command'''s with the following '''keyword'''s will be used for '''animation'''s.
 
|'''Jmol script command'''s with the following '''keyword'''s will be used for '''animation'''s.
  
 
|-
 
|-
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|00:24
 
|'''move, delay, slab, loop '''and''' capture'''.
 
|'''move, delay, slab, loop '''and''' capture'''.
  
 
|-
 
|-
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| 00:30
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|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'''.
  
 
|-
 
|-
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| 00:39
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|00:39
 
|If not, for relevant tutorials, please visit our website.  
 
|If not, for relevant tutorials, please visit our website.  
  
 
|-
 
|-
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| 00:44
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|00:44
 
|To record this tutorial, I am using '''Ubuntu OS''' version 14.10,
 
|To record this tutorial, I am using '''Ubuntu OS''' version 14.10,
  
 
|-
 
|-
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| 00:51
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|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
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|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
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|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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|-
 
|-
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| 01:17
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|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.
  
 
|-
 
|-
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| 01:23
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|01:23
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|'''loop '''command causes the script to restart at the beginning with an optional  
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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
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|01:30
 
|'''capture '''command captures animations as animated '''GIF''' files.
 
|'''capture '''command captures animations as animated '''GIF''' files.
  
 
|-
 
|-
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| 01:36
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|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'''.  
  
 
|-
 
|-
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| 01:44
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|01:44
 
|Let us open the Jmol window and demonstrate an animation using '''move''' command.  
 
|Let us open the Jmol window and demonstrate an animation using '''move''' command.  
  
 
|-
 
|-
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| 01:50
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|01:50
 
|I will begin with a simple '''move''' command using ethane as an example.
 
|I will begin with a simple '''move''' command using ethane as an example.
  
 
|-
 
|-
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| 01:55
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|01:55
 
|Create a model of '''ethane''' using '''modelkit''' menu.
 
|Create a model of '''ethane''' using '''modelkit''' menu.
  
 
|-
 
|-
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| 01:59
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|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'''.
  
 
|-
 
|-
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| 02:06
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|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.
  
 
|-
 
|-
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| 02:13
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|02:13
 
|Open the '''console''' using '''File''' menu.
 
|Open the '''console''' using '''File''' menu.
  
 
|-
 
|-
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| 02:17
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|02:17
 
|At the prompt, type the following command.
 
|At the prompt, type the following command.
  
 
|-
 
|-
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| 02:21
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|02:21
 
|The '''command line''' starts with the word "move"
 
|The '''command line''' starts with the word "move"
  
 
|-
 
|-
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| 02:24
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|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.  
  
 
|-
 
|-
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| 02:29
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|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.
  
 
|-
 
|-
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| 02:36
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|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,
−
 
+
−
4<sup>th</sup> is the '''zoom modifier''', expressed in positive or negative numbers,
+
  
 
|-
 
|-
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| 02:48
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|02:48
 
|positive for '''zoom in''' and negative for '''zoom out'''.
 
|positive for '''zoom in''' and negative for '''zoom out'''.
  
 
|-
 
|-
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| 02:52
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|02:52
 
|The next three parameters deal with '''translation''' along the three axes.
 
|The next three parameters deal with '''translation''' along the three axes.
  
 
|-
 
|-
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| 02:57
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|02:57
 
|8th is the '''slab''' parameter. Slab '''slice'''s the molecule.  
 
|8th is the '''slab''' parameter. Slab '''slice'''s the molecule.  
  
 
|-
 
|-
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| 03:03
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|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.
  
 
|-
 
|-
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| 03:10
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|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.
  
 
|-
 
|-
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| 03:17
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|03:17
 
|Back to the '''Jmol''' panel.
 
|Back to the '''Jmol''' panel.
  
 
|-
 
|-
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| 03:20
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|03:20
 
|Press '''Enter''' and observe the panel.
 
|Press '''Enter''' and observe the panel.
  
 
|-
 
|-
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| 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.
  
 
|-
 
|-
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| 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.
  
 
|-
 
|-
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| 03:36
+
|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.  
  
 
|-
 
|-
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| 03:48
+
|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.  
  
 
|-
 
|-
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| 04:06
+
|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.
  
 
|-
 
|-
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| 04:15
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|04:15
 
|'''Edit''' the command as I have shown here, on the console.
 
|'''Edit''' the command as I have shown here, on the console.
  
 
|-
 
|-
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| 04:19
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|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
+
|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
+
|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
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|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
+
|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.
  
 
|-
 
|-
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| 05:21
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|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
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|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
+
|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
+
|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
+
|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
+
|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
+
|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.
  
 
|-
 
|-
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| 06:48
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|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
+
|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
+
|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
+
|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
+
|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.

Contributors and Content Editors

PoojaMoolya, Pratik kamble, Sandhya.np14

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