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

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|-
 
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| 00:24
 
| 00:24
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|'''Move, delay, slab, loop '''and''' capture'''.
+
|'''move, delay, slab, loop '''and''' capture'''.
  
 
|-
 
|-
 
|  00:30
 
|  00:30
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|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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|-
 
|-
 
|01:11  
 
|01:11  
−
|'''delay '''command is used to pause a script for the specified number of seconds.
+
|'''delay '''command is used to pause a '''script''' for the specified number of seconds.
  
 
|-
 
|-
 
| 01:17
 
| 01:17
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|'''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
 
|  01:23
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|'''loop '''command causes the script to restart at the beginning, with an optional  
+
|'''loop '''command causes the script to restart at the beginning, with an optional  
 
time delay.
 
time delay.
  
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|-
 
|-
 
|  01:59
 
|  01:59
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|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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|-
 
|-
 
|  02:13
 
|  02:13
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|Open the console using file menu.
+
|Open the '''console''' using '''File''' menu.
  
 
|-
 
|-
 
|  02:17
 
|  02:17
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|At the prompt type the following command.
+
|At the prompt, type the following command.
  
 
|-
 
|-
 
| 02:21
 
| 02:21
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|The command line starts with the word '''move.'''
+
|The '''command line''' starts with the word '''move'''
  
 
|-
 
|-
 
| 02:24
 
| 02:24
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|Followed by numbers that quantify a set of animation parameters.  
+
|followed by numbers that quantify a set of animation parameters.  
  
 
|-
 
|-
 
| 02:29
 
| 02:29
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|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
 
|  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.  
  
 
4<sup>th</sup> is 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
 
| 02:48
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|Positive for zoom in and negative for zoom out.
+
|Positive for '''zoom in''' and negative for '''zoom out'''.
  
 
|-
 
|-
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|-
 
|-
 
| 02:57
 
| 02:57
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|8th is the '''slab''' parameter. Slab "slices" the molecule.  
+
|8th is the '''slab''' parameter. Slab '''slice'''s the molecule.  
  
 
|-
 
|-
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|-
 
|-
 
|  03:10
 
|  03:10
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|Parameter 9 is the amount of time, in seconds, taken in performing the move command.
+
|Parameter 9 is the amount of time, in seconds, 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 one.
+
|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
 
|  03:36
−
|Type '''delay''' space 2 after the semicolon.
+
|Type: '''delay space 2''' after the semicolon.
  
 
|-
 
|-
 
| 03:41
 
| 03:41
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|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
 
|  03:48
−
|Then type another '''move''' command after this delay command.
+
|Then type another '''move''' command after this '''delay''' command.
  
 
|-
 
|-
 
| 03:52
 
| 03:52
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|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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|-
 
|-
 
| 04:10
 
| 04:10
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|Again press up arrow key to get the previous command.
+
|Again press up-arrow key to get the previous command.
  
 
|-
 
|-
 
|  04:15
 
|  04:15
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|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
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|Use '''select''' key words to change the color of the hydrogens and carbons.
+
|Use '''select''' key words to change the color of the hydrogens and carbons. Press '''Enter
−
 
+
'''.
−
press enter
+
−
 
+
 
|-
 
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|  04:27
 
|  04:27
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|-
 
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|  04:41
 
|  04:41
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|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.
  
 
|-
 
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|  04:47
 
|  04:47
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|Type '''slab on''' after the '''select''' command.
+
|Type: "slab on" after the '''select''' command.
  
 
|-
 
|-
 
| 04:51
 
| 04:51
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|Type '''slab off''' at the end of the command.
+
|Type: "slab off" at the end of the command.
  
 
|-
 
|-
 
| 04:55
 
| 04:55
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|Press enter and observe the panel.  
+
|Press '''Enter''' and observe the panel.  
  
 
|-
 
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|-
 
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|  05:06
 
|  05:06
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|You can save this animation as a '''GIF''' file using '''capture''' key word.
+
|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.
  
 
|-
 
|-
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|-
 
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|  05:26
 
|  05:26
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|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'''.
  
 
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|-
 
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| 05:44
 
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|Open the saved '''GIF''' file with image viewer software.
+
|Open the saved '''GIF''' file with '''Image Viewer''' software.
  
 
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|  05:54
 
|  05:54
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|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.'''
  
 
|-
 
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|  06:06
 
|  06:06
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|Download the structure directly from '''pdb''' '''database''' using file menu.  
+
|Download the structure directly from '''pdb''' database using '''File''' menu.  
  
 
|-
 
|-
 
| 06:11
 
| 06:11
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|Type the '''pdb code''' in the text box, '''2DN1'''. Press ok.
+
|Type the '''pdb code''' in the text-box, "2DN1". Press '''OK'''.
  
 
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| 06:23
 
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|Type the following command in the '''Console .'''
+
|Type the following command in the '''Console.'''
  
 
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|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
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|Press enter and observe the panel.
+
|Press '''Enter''' and observe the panel.
  
 
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| 07:13
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|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.
  
 
|-
 
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| 07:20
 
| 07:20
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|"'''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'''.
  
 
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| 07:39
 
| 07:39
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|Now, Lets 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'''.
  
 
|-
 
|-
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|  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/>  
  
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|-
 
|-
 
| 08:17
 
| 08:17
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|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.  
  
 
|-
 
|-
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|-
 
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| 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.  
  
 
|}
 
|}

Revision as of 11:27, 12 February 2016

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 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 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 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 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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