[Biopython-dev] PDB occupancy behavior

Morten Kjeldgaard mok at bioxray.dk
Fri Aug 9 08:39:55 UTC 2013

Lenna wrote:

>  In summary, I am using software-produced PDB files that simply stop after
>  the coordinate data, so occupancy data is missing. Currently, the Biopython
>  PDBParser sets missing or blank occupancy to 0.0. I am suggesting changing
>  this to 1.0.

I think it is an incorrect default behaviour to set the occupancy to 1 if it's not present in the file. If the occupancy is not there, you can't say anything about it, and it should be set to 0, so the current defaults are correct IMO.

If, for some reason, you NEED the occupancy to be 1, and it is not, it is very simple to write a loop modifying it. I.e. special needs should be taken care of in the users program, not Bio.PDB.


Morten Kjeldgaard, asc. professor, MSc, PhD
Dept. of Molecular Biology and Genetics, Aarhus University
Gustav Wieds Vej 10C, Building 3135, DK-8000 Aarhus C, Denmark.

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