[Biopython] Writing into a PDB file using PDBIO module

[life happy]

Hi there,

I am new to Biopython and have been working for a couple of weeks on Bio.PDB
module.I would appreciate any clue or help in the following matter.

I have some short ,closely related peptide sequences.I want to align these
short peptides and send the aligned structures into a new PDB file.I used
set_atoms class in Superimposer module to align the short peptides. I tried
using PDBIO module, and send the aligned structures into a new PDB file. But
when I see the output PDB file, I get the whole proteins not the short
peptides. I like to have output PDB file with all the short peptides aligned
to any particular short peptide.


#This is the part of my code. B is list of atoms of peptides. C is a list
with PDB ids of each peptide.

from Bio.PDB.Superimposer import Superimposer
fixed = B[0:1*(stop-start+1)]
sup = Superimposer()
for i in range(1,5) :
        moving = B[i*(stop-start+1):(i+1)*(stop-start+1)]
        sup.set_atoms(fixed, moving)
        print "RMS(%s file %s chain, %s file %s model) = %0.2f" %
(C[0][0].split("'")[1],C[0][2].split("'")[1],C[i][0].split("'")[1],C[i][2].split("'")[1],
sup.rms)
        print "Saving %s aligned structure as PDB file %s" %
(C[0][2].split("'")[1], pdb_out_filename)
        io=Bio.PDB.PDBIO()
        io.set_structure(structure)
        io.save(pdb_out_filename)

thanks in advance!!

cheers,
Kumar.