Colorbydisplacement

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

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