[Biopython] Antwort: Re: PDB parsing

[Paul.Czodrowski at merck.de]

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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