[Biopython-dev] [Biopython] PDB occupancy behavior

[Peter Cock]

Thanks everyone - that seems like a clear consensus, patch applied :)

Peter

On Thu, Aug 8, 2013 at 9:30 PM, Sampson, Jared <Jared.Sampson at nyumc.org> wrote:
> Thanks, Lenna and João -
>
> I also agree, 1.0 is a better default occupancy value.  For most
> structural manipulation purposes, unless specified otherwise, we must assume
> the atoms listed are present in the structure at full occupancy.  Setting a
> reduced occupancy can be useful for partially bound ligands, disordered
> loops, and so forth, but doing so is the exception, not the rule.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> Old Public Health Building, Room 610
> 341 East 25th Street
> New York, NY 10016
> 212-263-7898
> http://kong.med.nyu.edu/
>
>
>
>
> On Aug 8, 2013, at 4:02 PM, João Rodrigues
> <anaryin at gmail.com<mailto:anaryin at gmail.com>> wrote:
>
> 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...
>
> Cheers,
>
> João
>
>
> 2013/8/8 Lenna Peterson <arklenna at gmail.com<mailto: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