Difference between revisions of "UCSF-Chimera/C2/Writing-Commands/English-timed"

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(Created page with "{| border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 |Welcome to this tutorial on '''Writing Commands '''in '''Chimera'''. |- | 00:06 |In this tutoria...")
 
 
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|-
 
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| 00:06
 
| 00:06
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|In this tutorial, we will type commands to-  Change the '''display''' to atoms.
+
|In this tutorial, we will type '''command'''s to-  change the '''display''' to atoms,
  
 
|-
 
|-
 
| 00:12
 
| 00:12
−
|  Show and hide '''ribbons'''.
+
|  show and hide '''ribbons''',
  
 
|-
 
|-
 
| 00:14
 
| 00:14
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|  Change the color of the '''amino acid residues.'''
+
|  change the color of the '''amino acid residues,'''
  
 
|-
 
|-
 
| 00:18
 
| 00:18
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|  Label individual '''residues'''.
+
|  label individual '''residues''',
  
 
|-
 
|-
 
| 00:21
 
| 00:21
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|  Remove '''solvent''' molecules.  And save the image in different file formats.
+
|  remove solvent molecules and '''save''' the '''image''' in different '''file format'''s.
  
 
|-
 
|-
 
| 00:28
 
| 00:28
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|To follow this tutorial you should have knowledge of-  Undergraduate '''Biochemistry'''
+
|To follow this tutorial, you should have knowledge of-  undergraduate '''Biochemistry''',
  
 
|-
 
|-
 
| 00:34
 
| 00:34
−
|  Must be familiar with, '''Structural Biology '''  and '''Chimera interface'''.  
+
|  must be familiar with '''Structural Biology '''  and '''Chimera interface'''.  
  
 
|-
 
|-
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|-
 
|-
 
| 00:44
 
| 00:44
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|To record this tutorial, I am using  '''Ubuntu OS version'''  14.04
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|To record this tutorial, I am using  '''Ubuntu OS''' version '''14.04''',
  
 
|-
 
|-
 
| 00:50
 
| 00:50
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|  '''Chimera''' '''version''' 1.10.2
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|  '''Chimera''' version '''1.10.2''',
  
 
|-
 
|-
 
| 00:53
 
| 00:53
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|  '''Mozilla firefox browser''' 42.0   And a working '''Internet connection'''.
+
|  '''Mozilla firefox browser 42.0'''  and a working internet connection.
  
 
|-
 
|-
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|-
 
|-
 
| 01:25
 
| 01:25
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|Tasks performed with '''menus '''can be carried out using '''commands'''.
+
|Tasks performed with menus can be carried out using '''commands'''.
  
 
|-
 
|-
 
| 01:31
 
| 01:31
−
|About '''Chimera Commands'''.
+
|About '''Chimera Commands'''-
  
 
|-
 
|-
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|-
 
|-
 
| 01:38
 
| 01:38
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|Multiple '''commands '''can be combined into one line with '''semicolon''' separators.
+
|Multiple '''commands '''can be combined into one line with semicolon separators.
  
 
|-
 
|-
 
| 01:43
 
| 01:43
−
|Press '''Enter key''' to execute the '''command'''.
+
|Press '''Enter''' key to '''execute''' the '''command'''.
  
 
|-
 
|-
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|-
 
|-
 
| 01:51
 
| 01:51
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|More information about '''commands''' is given at the link shown.  
+
|More information about '''commands''' is given at the '''link''' shown.  
  
 
|-
 
|-
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|-
 
|-
 
| 02:06
 
| 02:06
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|On the '''command line''' text box, type- '''open space 1zik'''.
+
|On the '''command line''' text box, type- '''"open space 1zik"'''.
  
 
|-
 
|-
 
| 02:13
 
| 02:13
−
|You need a working '''Internet connection''' for this step.
+
|You need a working internet connection for this step.
  
 
|-
 
|-
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|-
 
|-
 
| 02:20
 
| 02:20
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|The structure appears on the screen.
+
|The structure appears on the '''screen'''.
  
 
|-
 
|-
 
| 02:23
 
| 02:23
−
|To change the '''ribbons''' display to '''atoms''', in the '''command line text box''' type: The''' command '''word''' display '''. Press '''Enter'''.  
+
|To change the '''ribbons''' display to '''atoms'''- in the '''command line text box''', type the '''command''' word '''display '''. Press '''Enter'''.  
  
 
|-
 
|-
 
| 02:34
 
| 02:34
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|We now have the structure of the '''protein''' in '''atoms display'''.  
+
|We now have the structure of the '''protein''' in '''atoms''' display.  
  
 
|-
 
|-
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|-
 
|-
 
| 02:42
 
| 02:42
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|To hide the '''ribbons'''- Type, the '''wave symbol''', also known as '''tilda, ''' followed by the '''command''' word '''ribbon.'''
+
|To hide the '''ribbons'''- type the wave symbol, also known as '''tilda, ''' followed by the '''command''' word '''ribbon.'''
  
 
|-
 
|-
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|-
 
|-
 
| 02:55
 
| 02:55
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|Here, '''tilda''' symbol followed by''' ribbon keyword''' hides the '''ribbons'''.
+
|Here, '''tilda''' symbol followed by''' ribbon''' keyword hides the '''ribbons'''.
 
Press '''Enter'''.
 
Press '''Enter'''.
  
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|For example, to change the color of all '''leucines''', type:
 
|For example, to change the color of all '''leucines''', type:
  
−
'''Color space yellow space colon''' followed by the three letter abreviation for the '''amino acid'''.
+
'''color space yellow space colon''' followed by the three letter abbreviation for the amino acid.
  
 
|-
 
|-
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|-
 
|-
 
| 03:28
 
| 03:28
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|Here '''color''' is '''command word''' with '''argument''' as '''yellow''' and the target is all''' leucines''' in the structure.
+
|Here, '''color''' is command word with '''argument''' as '''yellow''' and the target is all''' leucines''' in the structure.
  
 
|-
 
|-
 
| 03:37
 
| 03:37
 
|If you do not specify a target, the entire structure will be colored in yellow.
 
|If you do not specify a target, the entire structure will be colored in yellow.
−
 
 
Press '''Enter'''.
 
Press '''Enter'''.
  
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|-
 
|-
 
| 03:51
 
| 03:51
−
|We can specifically color an '''amino acid''' present at a particular location.
+
|We can specifically color an amino acid present at a particular location.
  
 
|-
 
|-
 
| 03:56
 
| 03:56
−
|For example to change the color of''' histidine,''' present at position 18 on '''chain B''', type -
+
|For example, to change the color of''' histidine,''' present at position 18 on '''chain B''', type -
−
 
+
 
'''color space red space colon18.B'''. Press '''Enter'''.  
 
'''color space red space colon18.B'''. Press '''Enter'''.  
  
 
|-
 
|-
 
| 04:13
 
| 04:13
−
|Observe the panel. '''histidine''' is now colored in''' red'''.
+
|Observe the panel. '''histidine''' is now colored in red.
  
 
|-
 
|-
 
| 04:19
 
| 04:19
−
|To change the display of the entire structure to '''CPK spacefill''', type '''rep '''
+
|To change the display of the entire structure to '''CPK spacefill''', type '''rep '''.
  
 
|-
 
|-
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| 04:39
 
| 04:39
 
|To bring back the structure to '''stick''' display, again type '''rep space stick'''
 
|To bring back the structure to '''stick''' display, again type '''rep space stick'''
−
 
 
Press''' Enter'''
 
Press''' Enter'''
  
 
|-
 
|-
 
| 04:50
 
| 04:50
−
|To hide the''' solvent''' molecules from the structure, type - '''del''' (for delete) '''space solvent'''
+
|To hide the solvent molecules from the structure, type - '''del''' (for delete) '''space solvent'''
−
 
+
 
Press '''Enter'''.  
 
Press '''Enter'''.  
  
 
|-
 
|-
 
| 05:02
 
| 05:02
−
|To activate '''residues''' for selection, use '''select command''' word.
+
|To activate '''residues''' for selection, use '''select''' command word.
  
 
|-
 
|-
 
| 05:08
 
| 05:08
−
|On the '''command line''' text box type, '''select space colon '''followed by the number and '''chain''' of the residue.
+
|On the '''command line''' text box type: '''select space colon '''followed by the number and '''chain''' of the '''residue'''.
  
 
|-
 
|-
 
| 05:18
 
| 05:18
−
|For example to activate the '''lysine''' present at the position 28, on''' chain B''' Type,'''select space colon '''followed by''' 28 dot B '''. Press '''Enter'''.
+
|For example, to activate the '''lysine''' present at the position 28, on''' chain B''', type:'''select space colon '''followed by''' 28 dot B '''. Press '''Enter'''.
  
 
|-
 
|-
 
| 05:34
 
| 05:34
−
|Now to show the '''label''' for the '''residue''' selected, type '''rlabel space sel'''
+
|Now, to show the '''label''' for the '''residue''' selected, type: '''rlabel space sel'''
−
 
+
 
Press '''Enter'''.
 
Press '''Enter'''.
  
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|-
 
|-
 
| 05:51
 
| 05:51
−
|To de-select the '''residue''' which we have selected earlier, press up arrow key to get the '''select command'''.
+
|To de-select the '''residue''' which we have selected earlier, press up-arrow key to get the '''select''' command.
  
 
|-
 
|-
 
| 05:59
 
| 05:59
−
|Type the '''tilda symbol''' at the beginning of the '''command'''. Press '''Enter'''.  
+
|Type the tilda symbol at the beginning of the '''command'''. Press '''Enter'''.  
  
 
|-
 
|-
 
| 06:05
 
| 06:05
−
|A list of '''keywords''' and '''command index''' is available in the '''Help menu'''.
+
|A list of keywords and '''command index''' is available in the '''Help menu'''.
  
 
|-
 
|-
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|-
 
|-
 
| 06:16
 
| 06:16
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|A '''web-page '''opens with the list of '''keywords''' to write '''commands'''.  
+
|A '''web-page '''opens with the list of keywords to write '''commands'''.  
  
 
|-
 
|-
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| 06:25
 
| 06:25
 
|If you want to change the background color from black to blue, type: '''background space solid space blue'''
 
|If you want to change the background color from black to blue, type: '''background space solid space blue'''
−
 
 
Press '''Enter'''.  
 
Press '''Enter'''.  
  
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|-
 
|-
 
| 06:57
 
| 06:57
−
|To hide the '''command line''', click on '''Hide command line''' option in the drop down.
+
|To hide the '''command line''', click on '''Hide command line''' option in the drop-down.
  
 
|-
 
|-
 
| 07:03
 
| 07:03
−
|There are many options to '''save '''the structure you have created. Open the '''File menu.'''
+
|There are many options to '''save '''the structure you have created. Open the '''File''' menu.
  
 
|-
 
|-
 
| 07:09
 
| 07:09
−
|You can: '''Restore a Session''', '''Save a Session'''
+
|You can: '''Restore a Session''', '''Save a Session''',
  
 
|-
 
|-
 
| 07:14
 
| 07:14
−
|Save the image in '''JPEG''' or '''PNG''' formats  
+
|save the image in '''JPEG''' or '''PNG''' formats,
  
 
|-
 
|-
 
| 07:19
 
| 07:19
−
|Save the image as '''PDB''' or '''Mol2''' files, '''Export''' the scene etc.  
+
|save the image as '''PDB''' or '''Mol2''' files, '''Export''' the scene etc.  
  
 
|-
 
|-
 
| 07:27
 
| 07:27
−
|For demonstration, let me save the image in '''JPEG''' format.
+
|For demonstration, let me '''save''' the '''image''' in '''JPEG''' format.
  
 
|-
 
|-
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|-
 
|-
 
| 07:56
 
| 07:56
−
|For demonstration, I will type 800 as width and 600 as height.
+
|For demonstration, I will type '''800''' as '''width''' and '''600''' as '''height'''.
  
 
|-
 
|-
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|-
 
|-
 
|08:17
 
|08:17
−
|In this tutorial we typed '''commands''' to, Change the '''display''' to '''atoms'''.
+
|In this tutorial, we typed '''commands''' to: change the '''display''' to '''atoms''',
  
 
|-
 
|-
 
| 08:22
 
| 08:22
−
| Show and hide '''ribbons'''.
+
| show and hide '''ribbons''',
  
 
|-
 
|-
 
| 08:25
 
| 08:25
−
| Change the color of the '''amino acid residues.'''  
+
| change the color of the '''amino acid residues,'''  
  
 
|-
 
|-
 
| 08:28
 
| 08:28
−
| '''Label '''individual '''residues'''.
+
| '''label '''individual '''residues''',
  
 
|-
 
|-
 
| 08:31
 
| 08:31
−
|Remove '''solvent molecules'''. Save the image in different file formats.
+
|remove '''solvent molecules''', save the image in different '''file format'''s.
  
 
|-
 
|-
 
|08:38
 
|08:38
−
|Now for the '''Assignment'''
+
|Now for the '''assignment''':
−
 
+
Type '''commands''' to- '''load''' the structure of '''Human oxy-hemoglobin''' ('''PDB code: 2dn1''').
−
Type '''commands''' to,  Load the structure of '''Human oxy-hemoglobin''' ('''PDB code: 2dn1''')
+
  
 
|-
 
|-
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|-
 
|-
 
| 08:56
 
| 08:56
−
| Remove the '''solvent molecules''' and Save the image in '''JPEG''' format.
+
| Remove the solvent molecules and save the image in '''JPEG''' format.
  
 
|-
 
|-
 
| 09:03
 
| 09:03
−
|Your completed '''assignment''' should look as follows.
+
|Your completed assignment should look as follows.
  
 
|-
 
|-
 
| 09:12
 
| 09:12
−
|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.  
  
 
|-
 
|-
 
| 09:19
 
| 09:19
−
|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.  
−
 
+
 
For more details, please write to us.  
 
For more details, please write to us.  
  
 
|-
 
|-
 
|09:29
 
|09:29
−
|Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.  
+
|Spoken Tutorial Project is funded by '''NMEICT, MHRD''', Government of India.  
  
 
|-
 
|-
 
| 09:35
 
| 09:35
−
|More information on this Mission is available at the link shown.
+
|More information on this mission is available at the '''link''' shown.
  
 
|-
 
|-
 
| 09:40
 
| 09:40
−
|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 12:39, 26 June 2018

Time
Narration
00:01 Welcome to this tutorial on Writing Commands in Chimera.
00:06 In this tutorial, we will type commands to- change the display to atoms,
00:12 show and hide ribbons,
00:14 change the color of the amino acid residues,
00:18 label individual residues,
00:21 remove solvent molecules and save the image in different file formats.
00:28 To follow this tutorial, you should have knowledge of- undergraduate Biochemistry,
00:34 must be familiar with Structural Biology and Chimera interface.
00:40 For relevant tutorials, please visit our website.
00:44 To record this tutorial, I am using Ubuntu OS version 14.04,
00:50 Chimera version 1.10.2,
00:53 Mozilla firefox browser 42.0 and a working internet connection.
01:00 Double-click on the Chimera icon to open the Chimera window.
01:06 Click on the lightning bolt icon to open the graphics window.
01:10 In this tutorial, I will demonstrate how to use commands to manipulate the structure.
01:16 Open the Command Line using Favorites menu.
01:20 A command text box appears at the bottom of the Chimera window.
01:25 Tasks performed with menus can be carried out using commands.
01:31 About Chimera Commands-
01:34 Chimera commands are entered at the Command line.
01:38 Multiple commands can be combined into one line with semicolon separators.
01:43 Press Enter key to execute the command.
01:47 Previous commands can be accessed from command History.
01:51 More information about commands is given at the link shown.
01:56 Back to the Chimera window. Let us open a model of leucine zipper by typing a command.
02:03 The command starts with a command word.
02:06 On the command line text box, type- "open space 1zik".
02:13 You need a working internet connection for this step.
02:17 Press Enter to execute the command.
02:20 The structure appears on the screen.
02:23 To change the ribbons display to atoms- in the command line text box, type the command word display . Press Enter.
02:34 We now have the structure of the protein in atoms display.
02:38 The structure is partially represented as ribbons.
02:42 To hide the ribbons- type the wave symbol, also known as tilda, followed by the command word ribbon.
02:51 A command with a tilda indicates the reverse function.
02:55 Here, tilda symbol followed by ribbon keyword hides the ribbons.

Press Enter.

03:03 We can use color command to set colors to atoms, bonds, surfaces etc.
03:10 For example, to change the color of all leucines, type:

color space yellow space colon followed by the three letter abbreviation for the amino acid.

03:24 For leucine, I will type leu.
03:28 Here, color is command word with argument as yellow and the target is all leucines in the structure.
03:37 If you do not specify a target, the entire structure will be colored in yellow.

Press Enter.

03:45 Observe the panel. All the leucines are now colored yellow.
03:51 We can specifically color an amino acid present at a particular location.
03:56 For example, to change the color of histidine, present at position 18 on chain B, type -

color space red space colon18.B. Press Enter.

04:13 Observe the panel. histidine is now colored in red.
04:19 To change the display of the entire structure to CPK spacefill, type rep .
04:26 rep is the truncated version for the keyword represent. rep space sphere ; press Enter.
04:37 Observe the panel.
04:39 To bring back the structure to stick display, again type rep space stick

Press Enter

04:50 To hide the solvent molecules from the structure, type - del (for delete) space solvent

Press Enter.

05:02 To activate residues for selection, use select command word.
05:08 On the command line text box type: select space colon followed by the number and chain of the residue.
05:18 For example, to activate the lysine present at the position 28, on chain B, type:select space colon followed by 28 dot B . Press Enter.
05:34 Now, to show the label for the residue selected, type: rlabel space sel

Press Enter.

05:44 Observe the panel. The residue label for the selected residue is displayed.
05:51 To de-select the residue which we have selected earlier, press up-arrow key to get the select command.
05:59 Type the tilda symbol at the beginning of the command. Press Enter.
06:05 A list of keywords and command index is available in the Help menu.
06:09 Click on the Help menu, scroll down and click on Commands index.
06:16 A web-page opens with the list of keywords to write commands.
06:22 Back to the Chimera window.
06:25 If you want to change the background color from black to blue, type: background space solid space blue

Press Enter.

06:38 The panel is now blue in color.
06:41 To view the Command history, click on the black triangle present at the right side of the Command line.
06:48 The Command history lists previously used commands.
06:53 Commands can be re-executed by clicking on the command.
06:57 To hide the command line, click on Hide command line option in the drop-down.
07:03 There are many options to save the structure you have created. Open the File menu.
07:09 You can: Restore a Session, Save a Session,
07:14 save the image in JPEG or PNG formats,
07:19 save the image as PDB or Mol2 files, Export the scene etc.
07:27 For demonstration, let me save the image in JPEG format.
07:33 Click on Save image option. A Save image dialog box opens.
07:40 Select the file location as Desktop.
07:44 Type the File name as 1zik. Choose the File type as JPEG.
07:52 Fix the image size according to your requirement.
07:56 For demonstration, I will type 800 as width and 600 as height.
08:05 Click on Save button. The image is saved as 1zik.jpg on the Desktop.
08:15 Let's summarize what we have learnt.
08:17 In this tutorial, we typed commands to: change the display to atoms,
08:22 show and hide ribbons,
08:25 change the color of the amino acid residues,
08:28 label individual residues,
08:31 remove solvent molecules, save the image in different file formats.
08:38 Now for the assignment:

Type commands to- load the structure of Human oxy-hemoglobin (PDB code: 2dn1).

08:48 Change the display to atoms and hide ribbons.
08:52 Color all histidine residues in green.
08:56 Remove the solvent molecules and save the image in JPEG format.
09:03 Your completed assignment should look as follows.
09:12 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

09:19 The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

09:29 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
09:35 More information on this mission is available at the link shown.
09:40 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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