Colorbydisplacement

Acknowledgement

This pymol script is made by Troels Emtekær Linnet.

This script is based on the scaffold from ColorByRMSD. Peace love and harmony goes to Shivender Shandilya and Jason Vertrees.

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, 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.

Code

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

There exist two versions.
ColorByDisplacementCA is quick and is between CA atoms. Ideal for helices representation.
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

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

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'

ColorByDisplacementCA O5NT, C5NT, resi 26-355, resi 26-355
ColorByDisplacementAll O5NT, C5NT, resi 26-355, resi 26-355

• 

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

• 

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

• 

  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 Pymol Script

cd C:\Users\tlinnet\Documents\My Dropbox\Speciale\5NT-project\Mutant-construct\Distance-Plot
#cd /homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/Distance-Plot
### load pdb files and rename
load 1HP1.pdb, O5NT-1HP1
load 1HPU.pdb, C5NT-1HPU

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

cartoon auto
show cartoon, O5NT
show cartoon, C5NT
set cartoon_fancy_helices=1
set bg,[1,1,1]

set auto_zoom, off

### Make sharper
set fog=0

### Load my function, and run function with input
run ColorByDisplacement.py
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

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 )

Python Code

This code has been put under version control. In the project, Pymol-script-repo.

For a color coded view:

https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/colorbydisplacement.py

See the raw code or download manually, by right clicking the following link here -> Save as: colorbydisplacement.py

https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/colorbydisplacement.py