[Biopython-dev] [Biopython (old issues only) - Bug #2780] (Resolved) PDB file HETATMs cannot be alternative location of a residue that is an ATOM

[redmine at redmine.open-bio.org]

Issue #2780 has been updated by Lenna Peterson.

Description updated
Status changed from New to Resolved
% Done changed from 0 to 100

Migrated to github:

https://github.com/biopython/biopython/issues/991

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Bug #2780: PDB file HETATMs cannot be alternative location of a residue that is an ATOM
https://redmine.open-bio.org/issues/2780#change-15368

* Author: Klaus Kopec
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.50
* URL: 
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In PDB files where HETATMs and ATOMs are altlocs of each other (e.g. 1RR2, residue 184), they are treated as two separate residues.

A obvious solution is to add an "else" case to the "if" in StructureBuilder.py line 115 (method init_residue(...)) that introduces some kind of mixed (HETATM as well as ATOM) DisorderedResidue.

The Main problem with that: the hetero field of the residue ids will differ between the residues, therefore the whole access-over-ids mechanism will most likely not work with these MixedDisorderedResidues as straight forward as it does so far.

Sadly, I could not come up with a good solution for this. Maybe some __getattr__ magic that alters the way Chains access their residues might work by allowing access to residues by only using the second and third component of the id 3-tuple?!

---Files--------------------------------
1rr2_residues184AB.pdb (1.66 KB)


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