[Biopython-dev] [Biopython - Bug #2951] (Closed) PDBParser assigns model 0 to first model no matter what...

[redmine at redmine.open-bio.org]

Issue #2951 has been updated by Eric Talevich.

Status changed from New to Closed
% Done changed from 0 to 100

Closed with this commit, as pointed out just now by Lenna Peterson:
https://github.com/biopython/biopython/commit/abdab1a1132ec811f9636f8ba805bbb6cda6dbe9

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Bug #2951: PDBParser assigns model 0 to first model no matter what...
https://redmine.open-bio.org/issues/2951

Author: TallPaul empty
Status: Closed
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 1.52
URL: 


I'm not sure if this is a bug or a feature, but PDBParser assigns the first model it sees as model 0 then increments that. This means someone thinking they are studying model X is actually studying X+1, and that assumes that authors always use sequential model numbers without skips. If authors CAN skip model number, ie, MODEL 2, then MODEL 4, then MODEL 5... then in biopython these be models 0,1, and 2 in the structure... yuck. 

If this needs to be maintained for posterity, I would suggest adding another field to capture the TRUE model number if it exists.

See lines 106 and 122 here:
http://github.com/biopython/biopython/blob/master/Bio/PDB/PDBParser.py#106

Paul


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