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

Tue May 10 07:05:50 EDT 2011

Dear Joao,

thanks for your help and the documentation link!
So far, I was aware of this documentation
http://biopython.org/DIST/docs/tutorial/Tutorial.html

wherein PDB parsing is only briefly covered.

And, yes, progress is faster now!

Cheers,
Paul

> 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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