biopython_superimposer_example

#!/usr/bin/env python

"""
Example to align two equivalent protein structures.
"""

from Bio.PDB import PDBParser, Superimposer

parser = PDBParser(QUIET=1)

protA = parser.get_structure('protA', 'pdb_xyzA.pdb')
protB = parser.get_structure('protB', 'pdb_xyzB.pdb')

equivalent_atoms = []
for resA in protA.get_residues():
  for chain in protB.get_chains():
    if resA.id in chain:
        # Align only CA-atoms
        if 'CA' in resA:
            ca_pair = (resA['CA'], chain[resA.id]['CA'])
            equivalent_atoms.append(ca_pair)

super_imposer = Superimposer()
ref_atoms, mobi_atoms = zip(*equivalent_atoms)
super_imposer.set_atoms(ref_atoms, mobi_atoms)

print "RMS = {0:.2f}".format(super_imposer.rms)