[Biopython] PDB occupancy behavior

[Sampson, Jared]

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
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