[Biopython] PDB Construction Error

[Bhima Auro van der Molen]

Hi Peter,

Thanks for the response.. I thought it might be a typo somewhere however I 
don't know enough about the BioPython code to fix it myself yet.. 

I am a bit curious that the is being raised is a PDB Construction error... 
As I said, I am storing DSSP data in the b-factor column, as is done using the 
hsexpo.py script, but in order to be thorough in a statistical analysis I need 
to randomise that data and assign it randomly to residues in the PDB file.. I 
am not making any changes to the atomic co-ordinates of any of the residues.. 
the only data that gets re-written in this process is the b-factor column.  
What would cause a PDBConstruction Error to be raised?

Thanks
Bhima


On Wednesday 05 May 2010 18:21:27 Peter wrote:
> Hi,
> 
> That is a combination of two issues. I made a typo in the error
> handler which has been fixed as Bug 3059 on 19 April and will
> be part of the soon to be released Biopython 1.54 final. See:
> 
> http://bugzilla.open-bio.org/show_bug.cgi?id=3059
> 
> http://github.com/biopython/biopython/commit/ed22f3ac17d910cf1956c2be1a9aec
> 9f6e3125a4
> 
> However, the underlying problem is that your PDB file apparently
> has something wrong with the coordinates...
> 
> Peter

> On Wed, May 5, 2010 at 5:20 PM, Bhima van der Molen <bav853 at bham.ac.uk> 
wrote:
> > Hi Everyone,
> > 
> > I am working on protein structure data, where I store solvent
> > accessibility data in the b-factor column of PDB files.
> > 
> > Recently I have encountered this error:
> >  structure = parser.get_structure('structure_id', fileName)
> >  File "/usr/lib/pymodules/python2.6/Bio/PDB/PDBParser.py", line 64, in
> > get_structure
> >    self._parse(file.readlines())
> >  File "/usr/lib/pymodules/python2.6/Bio/PDB/PDBParser.py", line 84, in
> > _parse
> >    self.trailer=self._parse_coordinates(coords_trailer)
> >  File "/usr/lib/pymodules/python2.6/Bio/PDB/PDBParser.py", line 159, in
> > _parse_coordinates
> >    raise PDBConstructionError("Invalid or missing coordinate(s) at line
> > %i." \
> > NameError: global name 'PDBContructionError' is not defined
> > 
> > Has anyone come across this before?  If so, is there a fix?

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