[Biopython-dev] [Bug 2780] New: PDB file HETATMs cannot be alternative location of a residue that is an ATOM
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Thu Mar 5 10:42:27 UTC 2009
http://bugzilla.open-bio.org/show_bug.cgi?id=2780
Summary: PDB file HETATMs cannot be alternative location of a
residue that is an ATOM
Product: Biopython
Version: 1.49
Platform: PC
OS/Version: Linux
Status: NEW
Severity: normal
Priority: P2
Component: Main Distribution
AssignedTo: biopython-dev at biopython.org
ReportedBy: klaus.kopec at tuebingen.mpg.de
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?!
--
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
More information about the Biopython-dev
mailing list