[Biopython] PDB Construction Error
Peter
biopython at maubp.freeserve.co.uk
Wed May 5 17:21:27 UTC 2010
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
More information about the Biopython
mailing list