[Biopython] PDB Construction Error

Bhima van der Molen bav853 at bham.ac.uk
Wed May 5 16:20:41 UTC 2010


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?

Thanks
Bhima




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