[BioPython] Problem to open PDBid 2mbw

Ismail Ekoprayitno Rozi eko at eijkman.go.id
Fri Dec 9 05:26:04 EST 2005


Hi,
I'm not so good in python and I'd like to use Bio.PDB (fromp biopython 1.41) in
my scripts.
When trying to open PDBid 2mbw, the error bellow is coming out (other PDBid
seems to be opened normally).
Any idea how to solve it?

Thanks for your help,
I. E. Rozi

-------------

Python 2.3.5 (#2, Aug 30 2005, 15:50:26)
[GCC 4.0.2 20050821 (prerelease) (Debian 4.0.1-6)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.PDB import PDBParser
>>> p = PDBParser(PERMISSIVE=1)
>>> structure = p.get_structure("2mbw","./pdb2mbw.ent")
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.3/site-packages/Bio/PDB/PDBParser.py", line 66, in
get_structure
    self._parse(file.readlines())
  File "/usr/lib/python2.3/site-packages/Bio/PDB/PDBParser.py", line 87, in
_parse
    self.trailer=self._parse_coordinates(coords_trailer)
  File "/usr/lib/python2.3/site-packages/Bio/PDB/PDBParser.py", line 179, in
_parse_coordinates
    structure_builder.init_residue(resname, hetero_flag, resseq, icode)
  File "/usr/lib/python2.3/site-packages/Bio/PDB/StructureBuilder.py", line 155,
in init_residue
    self.chain.add(residue)
  File "/usr/lib/python2.3/site-packages/Bio/PDB/Entity.py", line 80, in add
    raise PDBConstructionException, "%s defined twice" % entity.get_full_id()
  File "/usr/lib/python2.3/site-packages/Bio/PDB/Entity.py", line 132, in
get_full_id
    parent=self.get_parent()
  File "/usr/lib/python2.3/site-packages/Bio/PDB/Entity.py", line 102, in
get_parent
    raise PDBException, 'No parent'
PDBException: No parent



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