ColorByRMSD

Type	Python Module
Download	colorbyrmsd.py
Author(s)	Shivender Shandilya, Jason Vertrees, Thomas Holder
License	BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

Introduction

This script allows you to color two structures by Root Mean Square Deviation (RMSD). The distances between aligned C-alpha atom pairs are stored as B-factors of these residues, which are colored by a color spectrum, with blue specifying the minimum pairwise RMSD and red indicating the maximum. Unaligned residues are colored gray.

Usage

colorbyrmsd mobile, target [, doAlign [, doPretty [, guide [, method ]]]]

Arguments

• mobile = string: atom selection for mobile atoms
• target = string: atom selection for target atoms
• doAlign = 0 or 1: Superpose selections before calculating distances {default: 1}
• doPretty = 0 or 1: Show nice representation and colors {default: 1}
• guide = 0 or 1: Only use C-alpha atoms {default: 1}
• method = align or super: Method to match atoms {default: super}

Examples

# example #1
colorbyrmsd 1cbs, 1hmt, doAlign=1, doPretty=1
# example #2
colorbyrmsd 1eaz, 1fao, doAlign=1, doPretty=1

• 

  1cbs and 1hmt aligned and colored by RMSD. Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.

• 

  1eaz and 1fao aligned and colored by RMSD. Dark blue is good alignment, higher deviations are in orange/yellow/red. Residues not used for alignment are colored white.