[Biopython] Antwort: Re: Antwort: Re: PDB parsing

[João Rodrigues]

Use PDBIO.

from Bio.PDB import PDBIO
IO = PDBIO()
IO.set_structure(your_structure)
IO.save(output_filename)

You can also control which parts of the structure to output with Select.

Check the documentation<http://www.biopython.org/DIST/docs/cookbook/biopdb_faq.pdf>,
it will make you progress much faster :)

Cheers,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



On Tue, May 10, 2011 at 11:32 AM, <Paul.Czodrowski at merck.de> wrote:

> Dear João,
>
>
> cool, thank you very much so far!
>
> How do I output the newly generated PDBfile?
>
> Cheers & thanks,
> Paul
>
>
>
> > Hey Paul,
> >
> > First of all, you should not call _parse on your own. That is called
> > already when you call get_structure(). Generally, if a method has an
> > underscore behind its name it means it shouldn't really be called
> > unless you really know what you want to do with it.
> >
> > What version of Biopython are you using?
> >
> > I'd do this:
>
> > structure_id = "1234"
> > PDBFILE = open(filename,'r')
> > p = PDBParser(PERMISSIVE=1)
> > pp = p.get_structure(structure_id, PDBFILE)
> >
> > for atom in pp.get_atoms():
> >  atom.bfactor = 10.0
> >  print atom.bfactor
> >
> > It works pretty well here, with version 1.57.
> >
> > Cheers,
> >
> > João [...] Rodrigues
> > http://nmr.chem.uu.nl/~joao
> >
> >
>
> > On Tue, May 10, 2011 at 11:19 AM, <Paul.Czodrowski at merck.de> wrote:
> > Dear Joao,
> >
> > this one does not work:
> > "
> >
> > structure_id = "1234"
> > PDBFILE = open(filename,'r').read()
> > p = PDBParser(PERMISSIVE=1)
> > p._parse(PDBFILE)
> > pp = p.get_structure(structure_id, PDBFILE)
> >
> >
> > for atom in pp.get_atoms():
> >  atom.bfactor = 10.0
> >  print atom.bfactor
> > "
> >
> >
> > "p.get_structure(structure_id, PDBFILE)" seems to get the structural
> data,
> > but setting the bfactor does not give any output.
> >
> >
> >
> >
> > Cheers & Thanks,
> > Paul
> >
> >
> > > Hey Paul,
> > >
> > > When you parse a PDB file with PDBParser it automatically retrieves
> both
> > > B-factor and occupancy. If it fails to do so for any reason, it
> defaults
> > > those values to 0.
> > >
> > > After parsing, you can set those values explicitly by modifying the
> > > corresponding attribute of the Atom object. So, for example, to change
> > the
> > > B-factor of all your atoms to 10.0, you just have to do:
> > >
> > > for atom in structure.get_atoms():
> > > >   atom.bfactor = 10.0
> > > >
> > >
> > > Hope this answered your question.
> > >
> > > Cheers,
> > >
> > > João [...] Rodrigues
> > > http://nmr.chem.uu.nl/~joao
> > >
> > >
> > >
> > > On Tue, May 10, 2011 at 9:50 AM, <Paul.Czodrowski at merck.de> wrote:
> > >
> > > >
> > > > Dear folks,
> > > >
> > > > how do I add a B-factor as well as an occupancy column to a PDB file?
> > > >
> > > > I guess Bio.PDB is the appropriate module.
> > > > But I already fail with regards to a simple PDB load...
> > > >
> > > >
> > > > Cheers,
> > > > Paul
> >
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