Difference between revisions of "Colorbydisplacement"

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== Acknowledgement ==
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{{Infobox script-repo
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This pymol script is made by Troels Emtekær Linnet.
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|type      = script
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|filename  = colorbydisplacement.py
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This script is based on the scaffold from [[ColorByRMSD]]. Peace love and harmony goes to Shivender Shandilya and Jason Vertrees.
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|author    = [[User:Tlinnet|Troels E. Linnet]]
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|license  = BSD
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}}
  
 
== Introduction ==
 
== Introduction ==
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This script allows you to color two structures by distance displacement between an Open and Closed form of a protein, as calculated by PyMol's internal distance command. The pairwise distance is calculated between, C-alpha or all-atoms. The distance displacement values are stored as B-factors of these residues, which are colored by a ''rainbow'' color spectrum, with blue specifying minimum  and red indicating maximum.
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This script allows you to color two structures by distance displacement between an Open and Closed form of a protein, as calculated by PyMol's internal distance command. The pairwise distance is calculated between all-atoms. The distance displacement values are stored as B-factors of these residues, which are colored by a ''rainbow'' color spectrum, with blue specifying minimum  and red indicating maximum.
  
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== Code ==
 
 
Do keep in mind, all original B-factors values are overwritten!
 
Do keep in mind, all original B-factors values are overwritten!
  
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There exist two versions. <br>
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There exist one version. <br>
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ColorByDisplacement'''CA''' is quick and is between CA atoms. Ideal for helices representation. <br>
 
 
ColorByDisplacement'''All''' is between All atoms in residues and is quite slow => 3-5 mins for a run. Ideal for sticks representation.
 
ColorByDisplacement'''All''' is between All atoms in residues and is quite slow => 3-5 mins for a run. Ideal for sticks representation.
  
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=== Examples ===
 
=== Examples ===
 
<syntaxhighlight lang="python">
 
<syntaxhighlight lang="python">
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ColorByDisplacementCA O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
 
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
  
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ColorByDisplacementCA O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t, AlignedWhite='no'
 
 
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t, AlignedWhite='no'
 
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t, AlignedWhite='no'
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ColorByDisplacementCA O5NT, C5NT, resi 26-355, resi 26-355
 
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ColorByDisplacementAll O5NT, C5NT, resi 26-355, resi 26-355
 
 
</syntaxhighlight>
 
</syntaxhighlight>
  
 
<gallery heights="240px" widths="340px">
 
<gallery heights="240px" widths="340px">
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Image:ColorByDisplacement-CA-1.png|ColorByDisplacementCA used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
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Image:ColorByDisplacement-CA-2.png|ColorByDisplacementCA used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
 
Image:ColorByDisplacement-All-1.png|ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
Image:ColorByDisplacement-All-1.png|ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
Image:ColorByDisplacement-All-2.png|ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
Image:ColorByDisplacement-All-2.png|ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.
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Residues not in both pdb files is colored black
 
Residues not in both pdb files is colored black
  
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== Example Pymol Script ==
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== Example 1 ==
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<syntaxhighlight lang="python">
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{{Template:PymolScriptRepoDownload|examples/colorbydisplacement_1.pml}}
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cd C:\Users\tlinnet\Documents\My Dropbox\Speciale\5NT-project\Mutant-construct\Distance-Plot
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<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/colorbydisplacement_1.pml" highlight="python" />
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#cd /homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/Distance-Plot
 
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### load pdb files and rename
 
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load 1HP1.pdb, O5NT-1HP1
 
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load 1HPU.pdb, C5NT-1HPU
 
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hide everything
 
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### Select asymmetric units from pdb file
 
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create O5NT, /O5NT-1HP1//A
 
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create C5NT, /C5NT-1HPU//C
 
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delete O5NT-1HP1
 
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delete C5NT-1HPU
 
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cartoon auto
 
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show cartoon, O5NT
 
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show cartoon, C5NT
 
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set cartoon_fancy_helices=1
 
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set bg,[1,1,1]
 
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set auto_zoom, off
 
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### Make sharper
 
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set fog=0
 
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### Load my function, and run function with input
 
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run ColorByDisplacement.py
 
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ColorByDisplacementCA O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
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#ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
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set_view (\
 
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    0.094686687,  -0.390707940,    0.915631354,\
 
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    0.809000611,  -0.505792081,  -0.299485058,\
 
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    0.580131471,    0.769104064,    0.268191338,\
 
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    0.000000000,    0.000000000, -280.940521240,\
 
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    26.240486145,  46.146961212,  21.702068329,\
 
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  231.830673218,  330.050415039,  -20.000000000 )
 
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</syntaxhighlight>
 
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== Python Code ==
 
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This code has been put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].
 
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You can see the code here:
 
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https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py
 
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Or download manually, by right clicking the following link here -> Save as: colorbydisplacement.py
 
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https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py
 
  
 
[[Category:Script_Library]]
 
[[Category:Script_Library]]
 
[[Category:Structural_Biology_Scripts]]
 
[[Category:Structural_Biology_Scripts]]
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[[Category:Pymol-script-repo]]

Latest revision as of 11:02, 15 January 2012

Type Python Script
Download colorbydisplacement.py
Author(s) Troels E. Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Introduction

This script allows you to color two structures by distance displacement between an Open and Closed form of a protein, as calculated by PyMol's internal distance command. The pairwise distance is calculated between all-atoms. The distance displacement values are stored as B-factors of these residues, which are colored by a rainbow color spectrum, with blue specifying minimum and red indicating maximum.

Do keep in mind, all original B-factors values are overwritten!

There exist one version.
ColorByDisplacementAll is between All atoms in residues and is quite slow => 3-5 mins for a run. Ideal for sticks representation.

You have to specify which residues should be used in the alignment procedure, or it will take all residues as standard

V.2 is implemented the 2011.01.06 - Due to a bug in coloring.

Bug in code

A bug in the boolean operator of the spectrum command has been found. This versions work for version 1.3 Educational product.
For other versions of pymol, try to change (comment/uncomment) the cmd.spectrum line. The other spectrum line works for Open-Source PyMOL 1.2r3pre, Incentive product

Examples

ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t

ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t, AlignedWhite='no'

  • ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.

  • ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.

Dark blue is low displacement, higher displacements are in orange/yellow/red.
Residues used for alignment is colored white. Can be turned off in top of algorithm. Residues not in both pdb files is colored black

Example 1

Download: examples/colorbydisplacement_1.pml
This code has been put under version control in the project Pymol-script-repo 
reinitialize
import colorbydisplacement

fetch 1HP1, async=0
fetch 1HPU, async=0

hide everything
### Select asymmetric units from pdb file
create O5NT, /1HP1//A
create C5NT, /1HPU//C
delete 1HP1
delete 1HPU

show cartoon, O5NT
show cartoon, C5NT

ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t

set_view (\
     0.094686687,   -0.390707940,    0.915631354,\
     0.809000611,   -0.505792081,   -0.299485058,\
     0.580131471,    0.769104064,    0.268191338,\
     0.000000000,    0.000000000, -280.940521240,\
    26.240486145,   46.146961212,   21.702068329,\
   231.830673218,  330.050415039,  -20.000000000 )
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