Finding distance from superimposed PDBs

[bio_informatics]

Hi Members,
How do I get distance between pdb atoms of 2 files, after they are super imposed?

def alignPDB_file(refPDB, samplePDB): # function to align pdb file
     ref_atoms,sample_atoms=[],[]
     sam_str=PDBParser(QUIET=True).get_structure("sample",samplePDB) # create sampple structure
     ref_model=PDBParser(QUIET=True).get_structure("reference",refPDB)[0] # get the 0th model

     sam_model=sam_str[0] # get the 0th model

     for ref_chain in ref_model:
          for ref_res in ref_chain:
               if not "CA" in ref_res:continue
               else:  ref_atoms.append(ref_res['CA']) 

     for sam_chain in sam_model:
          for sam_res in sam_chain:
               if not "CA" in sam_res: continue
               else: sample_atoms.append(sam_res['CA'])

     sup=Superimposer()
     sup.set_atoms(ref_atoms, sample_atoms)

     print sup.rms
     sup.apply(sample_atoms)

     io = PDBIO() #PDBParser(QUIET=True).get_structure("reference",refPDB)
     io.set_structure(sam_str)
     io.save('out.pdb')

After superimposition, I want distance between atoms of file1, and file2.

Any suggestion(s)?

[maubp]

You are using Biopython (although you didn't say so). This might help: http://www.warwick.ac.uk/go/peter_co...n_contact_map/

[bio_informatics]

@maubp
Yes, I'm using Biopython and biopdb package from it.
Thanks for the very informative URL.

But, I wish to calculate distances after super imposition.

[GenoMax]

While not the answer you are looking for, I know that you are able to determine these distances using PyMOL. You can certainly do it interactively but I am not sure if you can do so programmatically.

If your institution does not have a license for PyMOL then you can try the education version here: http://pymol.org/educational/

[maubp]

See also http://www.warwick.ac.uk/go/peter_co...superposition/ for doing superposition of PDB files in Biopython.

But calculating the distances should be the same idea in either case.

[bio_informatics]

@maubp
I used the same concept, line(s) of code.
I guess, after super imposition, if I print sample pdb's new coordinates and then read through it, that might solve the purpose.

Any thoughts over it?