[Biopython-dev] [Bug 3096] PPBuilder build_peptides bugs

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3096





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2010-08-26 09:13 EST -------
(In reply to comment #3)
> Hi Peter,
> 
> I manage to produce the problem without modifying _accept().
> 

Excellent - that should help.

> 
> The output peptides should be: ['IHR',STGL'] not ['IHRXTGL'] in the current
> version...
>

I agree that ['IHRXTGL'] is definitely wrong (you have convinced me this
is a real bug).

Chain A has residues: ILE, HIS, ARG, XLY, SER, THR, GLY, LEU. Sensible
results are therefore ['IHRXSTGL'] if we include XLY as a modified amino
acid, or ['IHR', 'STGL'] is we exclude XLY (which we probably should).

Was XLY just an artifical example for this bug report? Looking at the
original PDB file for 1BFE, it is a modified GLY where you have switched
CA (alpha carbon) to the non-standard CX.

> Residue XLY A 319 or X in the fourth position should not be included
> since it doesn't have CA atom. Instead the current version includes it and
> remove the 'S' next to it, due to the same bug. One can get the right version
> using the patch provided before.
> 
> Whether the _accept is modified or not the bug remains. Also the user should
> not be expected to also modify build_peptides() method whenever PPBuilder
> _accept is modified since the accept variable in build_peptides isn't really a
> local (private) variable: In line 277 this variable accept is referenced from
> self.accept of PPBuilder.
>
> http://www.biopython.org/DIST/docs/api/Bio.PDB.Polypeptide-pysrc.html
> 277          accept=self._accept 

I'm assuming you mean the line "accept=self._accept" in the build_peptides
method of the _PPBuilder class in Bio/PDB/Polypeptide.py (the line numbers
have changed). If so, all that does is define a local variable within the
scope of that method - it does not expose the method in any way. I don't
understand what you mean here.

Peter


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