rmsd

protein-science - Scripts and Tools

RMSD

Sebastian Raschka, 09/01/2014
** Version 1.0**

---

I would be happy to hear your comments and suggestions. Please feel free to drop me a note via [twitter](https://twitter.com/rasbt), [email](mailto:[email protected]), or [google+](https://plus.google.com/+SebastianRaschka).

---

The rmsd.py script calculates the root mean square deviation (RSMD) in Angstrom between two structures in PDB format.
Note that both PDB files have to contain the same number of atoms for the script to work.

The RMSD measures the average distance between atoms of 2 protein or ligand structures via the equation

where a_i refers to the atoms of molecule 1, and b_i to the atoms of molecule 2, respectively. The subscripts x, y, z are denoting the x-y-z coordinates for every atom.

The RMSD is most commonly calculated without taking hydrogen-atoms into consideration (typically only C-alpha or main-chain atoms in proteins).

Requirements:

• Python 2.7.x or Python 3.x

Usage:

run python rmsd.py --help for the usage information:

usage: rmsd.py [-h] [-l] [-c] [-ca] PDBfile1 PDBfile2

The RMSD measures the average distance between atoms 
of 2 protein or ligand structures.
By default, all atoms but hydrogen atoms of the protein are included in the RMSD calculation.
NOTE: Both structures must contain the same number of atoms in similar order.

positional arguments:
  PDBfile1
  PDBfile2

optional arguments:
  -h, --help     show this help message and exit
  -l, --ligand   Calculates RMSD between ligand (HETATM) atoms.
  -c, --carbon   Calculates the RMSD between carbon atoms only.
  -ca, --calpha  Calculates the RMSD between alpha-carbon atoms only.

Example:
rmsd.py ~/Desktop/pdb1.pdb ~/Desktop/pdb2.pdb
0.7377

Example 1: RMSD of 2 ligand poses

command:

python rmsd.py pose1.pdb pose2.pdb --ligand

output:

1.9959

Example 2: between 2 peptides

command:

python rmsd.py peptide1.pdb peptide.pdb

output:

0.7377