[Biopython] PDB Construction Error

[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?

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/ed22f3ac17d910cf1956c2be1a9aec9f6e3125a4

However, the underlying problem is that your PDB file apparently
has something wrong with the coordinates...

Peter