[Biopython] PDB parsing

João Rodrigues anaryin at gmail.com
Tue May 10 08:30:04 UTC 2011

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.


João [...] Rodrigues

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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