[Biopython] PDB occupancy behavior

Sampson, Jared Jared.Sampson at nyumc.org
Thu Aug 8 20:30:31 UTC 2013

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.


Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016

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...



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.


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.


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