bioinformatics - Superposing DNA - Biology

Try this out with BioPython:

from Bio.PDB.PDBSuperimposer import PDBSuperimposer as superimposer
from Bio.PDB.PDBParser import PDBParser

parser = PDBParser()
sup = superimposer()
struct_1 = parser.get_structure("XXXX","first_pdb")
struct_2 = parser.get_structure("XXXX","second_pdb")

atoms1 = struct_1.get_atoms()
atoms2 = struct_2.get_atoms()
sup.set_atoms(atoms1,atoms2)

print sup.rotrans #print the rotation translation matrix from the SVD

#then to complete the alignment
sup.apply()  

You can look here for further details. SuperPoser