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

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(Created page with "{| style="border-spacing:0;" ! <center>Visual Cue</center> ! <center>Narration</center> |- | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;b...")
 
 
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'''Learning Objectives'''
 
'''Learning Objectives'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will type commands to,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, we will type commands to-
  
 
* Change the '''display''' to atoms.
 
* Change the '''display''' to atoms.
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'''Pre-requisites'''
 
'''Pre-requisites'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should have knowledge of,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial you should have knowledge of-
  
−
Undergraduate '''Biochemistry'''
+
*Undergraduate '''Biochemistry'''
  
−
Must be familiar with, '''Structural Biology '''
+
*Must be familiar with, '''Structural Biology '''
  
−
and '''Chimera interface'''.  
+
*and '''Chimera interface'''.  
  
 
For relevant tutorials, please visit our website.  
 
For relevant tutorials, please visit our website.  
Line 49: Line 49:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial, I am using
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To record this tutorial, I am using
  
−
'''Ubuntu OS version'''. 14.04
+
*'''Ubuntu OS version'''. 14.04
  
−
'''Chimera''' '''version''' 1.10.2
+
*'''Chimera''' '''version''' 1.10.2
  
−
'''Mozilla firefox browser''' 42.0
+
*'''Mozilla firefox browser''' 42.0
  
−
And a working '''Internet connection'''.
+
*And a working '''Internet connection'''.
  
 
|-
 
|-
Line 71: Line 71:
 
Click on''' Favorites''' menu, scroll down.
 
Click on''' Favorites''' menu, scroll down.
  
−
Click on C'''ommand line '''option.
 
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial,
 
  
−
I will demonstrate how to use '''commands''' to manipulate the structure.  
+
Click on '''Command line '''option.
 +
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial, I will demonstrate how to use '''commands''' to manipulate the structure.  
 +
 
  
 
Open the '''Command Line''' using '''Favorites''' menu.
 
Open the '''Command Line''' using '''Favorites''' menu.
Line 83: Line 83:
  
 
Cursor on the '''Command line'''.
 
Cursor on the '''Command line'''.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''command text box''' appears at the bottom of the C'''himera''' window.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''command text box''' appears at the bottom of the '''Chimera''' window.
  
  
−
Tasks, performed with '''menus '''can be carried out using '''commands'''.
+
Tasks performed with '''menus '''can be carried out using '''commands'''.
  
 
|-
 
|-
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''Chimera Commands'''.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| About '''Chimera Commands'''.
  
−
'''Chimera commands''' are entered at the''' Command line.'''
+
*'''Chimera commands''' are entered at the''' Command line.'''
  
−
Multiple '''commands '''can be combined into one line with '''semicolon''' separators.
+
*Multiple '''commands '''can be combined into one line with '''semicolon''' separators.
  
−
Press '''Enter key''' to execute the '''command'''.
+
*Press '''Enter key''' to execute the '''command'''.
  
 
|-
 
|-
Line 122: Line 122:
  
  
−
On the command line text box type,  
+
On the '''command line''' text box, type-
  
 
'''open space 1zik'''.
 
'''open space 1zik'''.
Line 131: Line 131:
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press enter.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press enter.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press''' enter''' to execute the '''command'''.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press''' Enter''' to execute the '''command'''.
  
 
The structure appears on the screen.
 
The structure appears on the screen.
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Press enter.
 
Press enter.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the '''ribbons''' display to atoms,  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the '''ribbons''' display to '''atoms''', in the '''command line text box''' type:
  
−
In the '''command line text box''' type:
+
*The''' command '''word''' display '''
  
−
The''' Command '''word''' display '''
+
*Press '''Enter'''.  
−
 
+
−
Press '''enter'''.  
+
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We now have the structure of the protein in atoms display.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We now have the structure of the '''protein''' in '''atoms display'''.  
  
 
The structure is partially represented as '''ribbons'''.
 
The structure is partially represented as '''ribbons'''.
Line 162: Line 160:
  
 
Press enter.
 
Press enter.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide the '''ribbons''',
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide the '''ribbons'''-
 +
 
 +
*Type, the '''wave symbol''', also known as '''tilda, '''
 +
*followed by the '''command''' word '''ribbon.'''
  
−
Type, the wave symbol, also known as '''tilda '''followed by the command word '''ribbon.'''
 
  
 
A '''command''' with a '''tilda''' indicates the reverse function.
 
A '''command''' with a '''tilda''' indicates the reverse function.
Line 170: Line 170:
 
Here, '''tilda''' symbol followed by''' ribbon keyword''' hides the '''ribbons'''.
 
Here, '''tilda''' symbol followed by''' ribbon keyword''' hides the '''ribbons'''.
  
−
press enter.
+
 
 +
Press '''Enter'''.
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can use color '''command''' to set colors to atoms, bonds, surfaces etc.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can use '''color command''' to set colors to '''atoms, bonds, surfaces''' etc.  
  
 
|-
 
|-
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−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For example to change the color of all '''leucines'''  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For example, to change the color of all '''leucines''', type:
  
−
Type:
+
*'''Color space yellow space colon''' :
 +
*followed by the three letter abreviation for the '''amino acid'''.
  
−
'''Color space yellow space colon''' :
+
For '''leucine''', I will type '''leu'''.
  
−
followed by the three letter abreviation for the amino acid.
 
−
 
−
For '''leucine''', I will type '''leu '''
 
−
 
−
Here '''color''' is '''command word''' with argument as yellow and 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.
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the command line.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the command line.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you do not specify a target the entire structure will be colored in yellow.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| If you do not specify a target, the entire structure will be colored in yellow.
  
−
Press '''enter '''
+
Press '''Enter'''.
  
−
Observe the '''panel'''. All the '''leucines''' are now colored yellow
+
Observe the '''panel'''. All the '''leucines''' are now colored yellow.
  
 
|-
 
|-
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can specifically color an '''amino acid''' present at a particular location.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can specifically color an '''amino acid''' present at a particular location.
  
−
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'''
 
'''color space red space colon18.B'''
  
−
Press enter
+
Press '''Enter'''.
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel, '''histidine''' is now colored in''' red'''.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel.
 +
 
 +
'''histidine''' is now colored in''' red'''.
  
 
|-
 
|-
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Press enter
 
Press enter
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the display of the entire structure to '''CPK '''spacefill,  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the display of the entire structure to '''CPK spacefill''', type '''rep '''
  
−
Type,
 
  
−
'''rep '''(rep is the truncated version for the keyword '''represent''' )
+
'''rep''' is the truncated version for the keyword '''represent'''.
  
−
rep '''space sphere'''
+
'''rep space sphere''' ; press '''Enter'''.
  
−
Press '''enter'''.
 
  
 
Observe the panel.
 
Observe the panel.
Line 250: Line 249:
  
 
press enter.
 
press enter.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To bring back the structure to '''stick''' display.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To bring back the structure to '''stick''' display, again type
−
 
+
−
Again type,
+
  
 
'''rep space stick'''
 
'''rep space stick'''
  
−
Press''' enter'''
+
Press''' Enter'''
  
 
|-
 
|-
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Press enter  
 
Press enter  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide the''' solvent''' molecules from the structure,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide the''' solvent''' molecules from the structure, type -
  
−
Type
+
'''del''' (for delete) '''space solvent'''
  
−
'''del for delete space solvent'''
+
Press '''Enter'''.  
−
 
+
−
Press enter.  
+
  
 
|-
 
|-
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−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To activate '''residues''' for selection, use '''select''' '''command''' word.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To activate '''residues''' for selection, use '''select command''' word.
  
 
On the '''command line''' text box type,
 
On the '''command line''' text box type,
  
−
'''Select space colon '''followed by the number and '''chain''' of the residue.
+
'''select space colon '''followed by the number and '''chain''' of the residue.
 +
 
  
 
For example to activate the '''lysine''' present at the position 28, on''' chain B'''  
 
For example to activate the '''lysine''' present at the position 28, on''' chain B'''  
Line 298: Line 294:
 
'''select space colon '''followed by''' 28 dot B '''
 
'''select space colon '''followed by''' 28 dot B '''
  
−
Press enter
+
Press '''Enter'''.
  
 
|-
 
|-
Line 307: Line 303:
  
 
Press enter
 
Press enter
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now to show the '''label''' for the '''residue''' selected,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now to show the '''label''' for the '''residue''' selected, type
−
 
+
−
Type
+
  
 
'''rlabel space sel'''
 
'''rlabel space sel'''
  
−
Press enter
+
Press '''Enter'''.
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel the '''residue label''' for the selected '''residue''' is displayed.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the panel.
 +
 
 +
 
 +
The '''residue label''' for the selected '''residue''' is displayed.
  
 
|-
 
|-
Line 325: Line 322:
  
 
'''~select :28.B '''
 
'''~select :28.B '''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To deselect the '''residue''' which we have selected earlier:
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To de-select the '''residue''' which we have selected earlier, press up arrow key to get the '''select command'''.
  
−
Press up arrow key to get the select '''command'''.
 
  
−
Type the '''tilda''' symbol at the beginning of the '''command'''.
+
Type the '''tilda symbol''' at the beginning of the '''command'''.
  
−
Press enter.  
+
Press '''Enter'''.  
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the commands index page.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the commands index page.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A list of keywords and '''command index''' is available in the '''Help menu'''.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A list of '''keywords''' and '''command index''' is available in the '''Help menu'''.
  
−
Click on the '''Help''' '''menu''', scroll down and click on '''Commands index'''.
+
Click on the '''Help menu''', scroll down and click on '''Commands index'''.
  
 
A '''web-page '''opens with the list of '''keywords''' to write '''commands'''.  
 
A '''web-page '''opens with the list of '''keywords''' to write '''commands'''.  
Line 349: Line 345:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to the '''Chimera''' window.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Back to the '''Chimera''' window.
  
−
If you want to change the background color from black to blue.
 
  
−
Type:
+
If you want to change the background color from black to blue, type:
  
 
'''background space solid space blue'''
 
'''background space solid space blue'''
  
−
Press enter.  
+
Press '''Enter'''.  
  
 
|-
 
|-
Line 363: Line 358:
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the black triangle present at the right side of the '''Command line'''.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the black triangle present at the right side of the '''Command line'''.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To view the '''Command''' History:
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To view the '''Command''' history, click on the black triangle present at the right side of the '''Command line'''.
−
 
+
−
 
+
−
Click on the black triangle present at the right side of the '''Command line'''.
+
−
 
+
  
 
|-
 
|-
Line 374: Line 365:
  
 
Click on any command.
 
Click on any command.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Command History''' lists previously used '''commands.'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The '''Command history''' lists previously used '''commands.'''
  
  
Line 381: Line 372:
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Hide command line''' option.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Hide command line''' option.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide the command line click on '''Hide command line''' option in the drop down.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To hide the '''command line''', click on '''Hide command line''' option in the drop down.
  
 
|-
 
|-
Line 394: Line 385:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| You can:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| You can:
  
−
'''Restore a Session'''
+
*'''Restore a Session'''
  
−
'''Save a Session'''
+
*'''Save a Session'''
  
−
Save the image in '''JPEG''' or '''PNG''' formats  
+
*Save the image in '''JPEG''' or '''PNG''' formats  
  
−
Save the image as '''PDB''' or '''Mol2''' files.
+
*Save the image as '''PDB''' or '''Mol2''' files
  
−
'''Export''' the scene etc.  
+
*'''Export''' the scene etc.  
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Save Image''' option.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Save Image''' option.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For demonstration let me save the image in '''JPEG''' format.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| For demonstration, let me save the image in '''JPEG''' format.
  
 
|-
 
|-
Line 417: Line 408:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Save image''' option.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Save image''' option.
  
−
'''Save image''' dialog box opens.
+
A '''Save image''' dialog box opens.
 +
 
  
 
Select the file location as '''Desktop'''.
 
Select the file location as '''Desktop'''.
 +
  
 
Type the '''File name '''as '''1zik'''.  
 
Type the '''File name '''as '''1zik'''.  
Line 437: Line 430:
 
For demonstration, I will type 800 as width and 600 as height.
 
For demonstration, I will type 800 as width and 600 as height.
  
−
Click on '''save''' button.
 
  
−
The image is saved as '''1zik.jpg''' on the '''desktop'''.
+
Click on '''Save''' button.
 +
 
 +
The image is saved as '''1zik.jpg''' on the '''Desktop'''.
  
 
|-
 
|-
Line 449: Line 443:
  
 
Summary
 
Summary
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial we typed commands to,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In this tutorial we typed '''commands''' to,
  
−
* Change the '''display''' to atoms.
+
* Change the '''display''' to '''atoms'''.
 
* Show and hide '''ribbons'''.
 
* Show and hide '''ribbons'''.
 
* Change the color of the '''amino acid residues.'''
 
* Change the color of the '''amino acid residues.'''
 
* '''Label '''individual '''residues'''.
 
* '''Label '''individual '''residues'''.
−
 
  
 
|-
 
|-
Line 463: Line 456:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|  
  
−
* Remove '''solvent '''molecules.
+
* Remove '''solvent molecules'''.
 
* Save the image in different file formats.
 
* Save the image in different file formats.
−
 
  
 
|-
 
|-
Line 473: Line 465:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now for the '''Assignment'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now for the '''Assignment'''
  
−
Type commands to,
+
Type '''commands''' to,
  
 
* Load the structure of '''Human oxy-hemoglobin''' ('''PDB code: 2dn1''')
 
* Load the structure of '''Human oxy-hemoglobin''' ('''PDB code: 2dn1''')
−
* Change the display to atoms and hide '''ribbons'''.  
+
* Change the display to '''atoms''' and hide '''ribbons'''.  
 
* Color all '''histidine residues''' in green.
 
* Color all '''histidine residues''' in green.
 
* Remove the '''solvent molecules'''.  
 
* Remove the '''solvent molecules'''.  
 
* Save the image in '''JPEG''' format.
 
* Save the image in '''JPEG''' format.
  
−
Your completed '''assignmet''' should look as follows.
+
Your completed '''assignment''' should look as follows.
  
 
|-
 
|-
Line 501: Line 493:
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.  
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.  
  
−
More information on this Mission is available at the link shown
+
More information on this Mission is available at the link shown.
  
 
|-
 
|-

Latest revision as of 15:02, 24 February 2016

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Writing Commands in Chimera.
Slide Number 2

Learning Objectives

In this tutorial, we will type commands to-
  • Change the display to atoms.
  • Show and hide ribbons.
  • Change the color of the amino acid residues.
  • Label individual residues.
Slide Number 3

Learning Objectives

  • Remove solvent molecules.
  • And save the image in different file formats.
Slide Number 4

Pre-requisites

To follow this tutorial you should have knowledge of-
  • Undergraduate Biochemistry
  • Must be familiar with, Structural Biology
  • and Chimera interface.

For relevant tutorials, please visit our website.

Slide Number 5

System Requirement

To record this tutorial, I am using
  • Ubuntu OS version. 14.04
  • Chimera version 1.10.2
  • Mozilla firefox browser 42.0
  • And a working Internet connection.
Click on the Chimera icon. Double-click on the Chimera icon to open the Chimera window.
Click on the lightning bolt icon. Click on the lightning bolt icon to open the graphics window.
Cursor on the panel.


Click on Favorites menu, scroll down.


Click on Command line option.

In this tutorial, I will demonstrate how to use commands to manipulate the structure.


Open the Command Line using Favorites menu.

Point to the command


Cursor on the Command line.

A command text box appears at the bottom of the Chimera window.


Tasks performed with menus can be carried out using commands.

Slide Number 6

Chimera Commands

About Chimera Commands.
  • Chimera commands are entered at the Command line.
  • Multiple commands can be combined into one line with semicolon separators.
  • Press Enter key to execute the command.
Slide number 7

Chimera Commands

Previous commands can be accessed from command History.

More information about commands is given at the link shown.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecore.html

Cursor on the command line. Back to the Chimera window.


Let us open a model of leucine zipper by typing a command.

On the command line text box type open 1zik. The command starts with a command word.


On the command line text box, type-

open space 1zik.


You need a working Internet connection for this step.

Press enter. Press Enter to execute the command.

The structure appears on the screen.

Type:

display

Press enter.

To change the ribbons display to atoms, in the command line text box type:
  • The command word display
  • Press Enter.
Cursor on the panel. We now have the structure of the protein in atoms display.

The structure is partially represented as ribbons.

Type:

~ ribbon


Press enter.

To hide the ribbons-
  • Type, the wave symbol, also known as tilda,
  • followed by the command word ribbon.


A command with a tilda indicates the reverse function.

Here, tilda symbol followed by ribbon keyword hides the ribbons.


Press Enter.

Cursor on the panel. We can use color command to set colors to atoms, bonds, surfaces etc.
Type:


color yellow :leu


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.

For leucine, I will type leu.


Here

  • color is command word with argument as yellow
  • and the target is all leucines in the structure.
Cursor on the command line. If you do not specify a target, the entire structure will be colored in yellow.

Press Enter.

Observe the panel. All the leucines are now colored yellow.

Cursor on the command line.

Type

color red :18.A

Press enter

We can specifically color an amino acid present at a particular location.


For example to change the color of histidine, present at position 18 on chain B, type -

color space red space colon18.B

Press Enter.

Cursor on the panel. Observe the panel.

histidine is now colored in red.

Type

rep sphere

Press enter

To change the display of the entire structure to CPK spacefill, type rep


rep is the truncated version for the keyword represent.

rep space sphere ; press Enter.


Observe the panel.

Type,

rep stick

press enter.

To bring back the structure to stick display, again type

rep space stick

Press Enter

Type

del solvent

Press enter

To hide the solvent molecules from the structure, type -

del (for delete) space solvent

Press Enter.

Type,

Select :18.A

Press enter


Type,

select :28.B


To activate residues for selection, use select command word.

On the command line text box type,

select space colon followed by the number and chain of the residue.


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.

Type

rlabel sel


Press enter

Now to show the label for the residue selected, type

rlabel space sel

Press Enter.

Cursor on the panel. Observe the panel.


The residue label for the selected residue is displayed.

press up arrow key to get the select command(select :28.B)

Type,

~select :28.B

To de-select the residue which we have selected earlier, press up arrow key to get the select command.


Type the tilda symbol at the beginning of the command.

Press Enter.

Scroll down the commands index page. A list of keywords and command index is available in the Help menu.

Click on the Help menu, scroll down and click on Commands index.

A web-page opens with the list of keywords to write commands.

Type:

background solid blue

Press enter.

Back to the Chimera window.


If you want to change the background color from black to blue, type:

background space solid space blue

Press Enter.

Cursor on the panel. The panel is now in blue color.
Click on the black triangle present at the right side of the Command line. To view the Command history, click on the black triangle present at the right side of the Command line.
Cursor on the Command history.


Click on any command.

The Command history lists previously used commands.


Commands can be re-executed by clicking on the command.

Click on Hide command line option. To hide the command line, click on Hide command line option in the drop down.
Click on File menu. Scroll down. There are many options to save the structure you have created.


Open the File menu.

Scroll down the File menu. You can:
  • Restore a Session
  • Save a Session
  • Save the image in JPEG or PNG formats
  • Save the image as PDB or Mol2 files
  • Export the scene etc.
Click on Save Image option. For demonstration, let me save the image in JPEG format.
Double click on “Desktop”.


Type the file name as 1zik.

File type as JPEG.

Click on Save image option.

A Save image dialog box opens.


Select the file location as Desktop.


Type the File name as 1zik.

Choose the File type as JPEG.

Type,

800 as image width and 600 as height.


Click on save button.

Fix the image size according to your requirement.


For demonstration, I will type 800 as width and 600 as height.


Click on Save button.

The image is saved as 1zik.jpg on the Desktop.

Cursor on the panel. Let's summarize what we have learnt.
Slide Number 8

Summary

In this tutorial we typed commands to,
  • Change the display to atoms.
  • Show and hide ribbons.
  • Change the color of the amino acid residues.
  • Label individual residues.
Slide Number 9

Summary

  • Remove solvent molecules.
  • Save the image in different file formats.
Slide Number 10

Assignment

Now for the Assignment

Type commands to,

  • Load the structure of Human oxy-hemoglobin (PDB code: 2dn1)
  • Change the display to atoms and hide ribbons.
  • Color all histidine residues in green.
  • Remove the solvent molecules.
  • Save the image in JPEG format.

Your completed assignment should look as follows.

Slide Number 11

Acknowledgement

The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

Slide Number 12 The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

Slide number 13 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this Mission is available at the link shown.

This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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