[Biopython] PDB parsing

[João Rodrigues]

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
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
> resulting from any unauthorized changes of the content of this message and
> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not guarantee that this message is free of viruses and does
> not accept liability for any damages caused by any virus transmitted
> therewith.
>
> Click http://disclaimer.merck.de to access the German, French, Spanish and
> Portuguese versions of this disclaimer.
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>