[Biopython] Writing into a PDB file using PDBIO module

[Peter]

Please keep the mailing list CC'd.

On Mon, Jul 20, 2009 at 11:59 PM, life happy<iitlife2008 at gmail.com> wrote:
> Yes! I have read this.

I'm glad you found that page (something I'd like to integrate into the
main Biopython Tutorial at some point):
http://www.warwick.ac.uk/go/peter_cock/python/protein_superposition/

> Which step applies the transformation?Isn't that
> set_atoms function? I am able to print RMS value. I did not follow the
> superimpose.apply(alt_model.get_atoms()) .

As the name should suggest, superimpose.apply(...) actually applies the
transformation. This is what you are missing. The set_atoms(...) just tells
the code which atoms are going to be superimposed.

> According to description in BioPDB faq pdf and
> http://www.biopython.org/DIST/docs/api/Bio.PDB.Superimposer%27.Superimposer-class.html
> set_atom does the transformation, right? If I am wrong, please correct me!

That docstring is rather confusing, we should fix that.

> Also,In which step are we sending the transformed co-ordinates into
> the PDB file?

These lines write out the PDB file for the whole structure:

io=Bio.PDB.PDBIO()
io.set_structure(structure)
io.save(pdb_out_filename)

> Also, the output PDB file has whole protein, I only want the short peptides
> aligned(only the atom lists that I gave as input must be aligned, not the
> whole protein of peptides).

If you only want some of the protein written, then you should only give
some of the structure to the PDB output code.

Peter