[Biopython-dev] [Biopython] PDB occupancy behavior

João Rodrigues anaryin at gmail.com
Thu Aug 8 20:02:39 UTC 2013

Hi Lenna,

As I mentioned in the Github email, I think it's fine. It doesn't matter if
the occupancy is 0 or 1 in case of a model most of the time. I agree with
it. The only bad thing I can think about is having occupancy for a certain
atom larger than 1 in some bogus cases but to be honest, no software that I
know of bothers checking that...



2013/8/8 Lenna Peterson <arklenna at gmail.com>

> Hi all,
> I just submitted a pull request I'd like wider feedback on.
> https://github.com/biopython/biopython/pull/207
> 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 would like to see if anyone knows of situations in which this would be a
> bad idea.
> Cheers,
> Lenna
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