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author: Yufeng Tong date: 2021-01-31 ...

A PyMOL script to calculate and display conformational changes

This is a PyMOL script to calculate the r.m.s.d. of two aligned structures with same residue numbering, for comparing the conformations of one protein in two different structures or two proteins (e.g. one wild type and one mutant) in two structures.

The script will create a copy of the target protein, replace the B-factor with the r.m.s.d. and generate a sausage display of the target protein.

Installation

Save the script to any folder accessible in PyMOL.

Usage

This script has been tested on PyMOL version 2.4.

1. Load two structures in the PyMOL program. Select polypeptide chains of interest, align them using PyMOL align or super command, and give them names, say mol1, and mol2
2. File → Run Script and load this script.
3. Run rmsdCA mol1, mol2, where mol1 is the reference structure, and mol2 is the target structure that will be colored.
4. A tgt_gzt object will be created and displayed in cartoon-sausage mode with a color ramp.
5. A pdb file rmsdBFactor_mol2.pdb will be generated and saved where the B-factor is the r.m.s.d. of the Cα atoms.
6. A csv file rmsdCA_mol2.csv will be generated and save where it tabulate the r.m.s.d per residue.

TODO