[Biopython] writing a PDB----PLEASEEEE HELP

[martin djokovic]

OK I have looked at both the tutorial and the link below
http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/python/protein_superposition/

I am pretty new so I am not sure how to do this.

I have 2 PDB files --lets call them A and B .

A = Bio.PDB.PDBParser().get_structure(pdb_code, pdb_filename)

B = Bio.PDB.PDBParser().get_structure(pdb_code2, pdb_filename2)

I pick the [CA] atoms of both these PDB's (each has 5 residues) then store
them in two lists called ref_atoms and alt_atoms respectively

super_imposer = Bio.PDB.Superimposer()
super_imposer.set_atoms(ref_atoms, alt_atoms)
super_imposer.apply(alt_atoms)
(I move the alt_atoms above)

Then write it out as follows

io=Bio.PDB.PDBIO()
io.set_structure(A)
io.save('ans.pdb')

My problem is I want a 3rd PDB  called 'ans.pdb' that has two structures,
namely A and B superimposed on each other but what I get is just a copy of A
in the 'ans.pdb'
What happened to the coordinates of B that I translated and rotated ?????

What am I doing wrong??
Thanks
Martin