[Biopython] PDB occupancy behavior
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.
Xiangpeng Kong Lab
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On Aug 8, 2013, at 4:02 PM, João Rodrigues <anaryin at gmail.com<mailto:anaryin at gmail.com>> wrote:
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>>
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
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