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

[Paul.Czodrowski at merck.de]

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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