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I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used.

I can superpose DNA molecules with Chimera, but I can't extract the translational distance and the rotational angle that was applied to superpose.

I have also had a look at MODELLER but it seems MODELLER cannot not superpose DNA.

Does anyone know of software/code by which I can extract the information I want?

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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

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