[Biopython-dev] Error on Bio.PDB

[Diego Zea]

One of the PDB (I have a very large dataset of PDB and there are a lot of them generating this kind of error) that give me the error is: http://www.rcsb.org/pdb/files/2ER9.pdb

Ant the error output is:
/usr/lib/pymodules/python2.7/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 2895.
  PDBConstructionWarning)
/usr/lib/pymodules/python2.7/Bio/PDB/StructureBuilder.py:85: PDBConstructionWarning: WARNING: Chain I is discontinuous at line 3216.
  PDBConstructionWarning)
Traceback (most recent call last):
  File "AsignarPDBaMIfile.py", line 45, in <module>
    cmap, pdb  = contactos_CB(pdb_file,pdb_cad,cutoff=1,n_salto=1)
  File "funciones_pdb.py", line 15, in contactos_CB
    cadena = model[cad]
  File "/usr/lib/pymodules/python2.7/Bio/PDB/Entity.py", line 38, in __getitem__
    return self.child_dict[id]
KeyError: 'A'

 
How Can be fixed?

P.D.: The lines of the firts warning are (at the beginig I wrote the number of lines for reference, I think that the TER line can be the cause of the problem but I'm not sure):

2893   ATOM   2455  N   PHE I   8      38.110 -15.236   4.503  0.89  0.76           N  
2894   TER    2456      PHE I   8                                                      
2895    HETATM 2457  O   HOH E 327      10.873  -3.134  11.448  0.89  0.01           O  








if ((dx*dp)>=(h/(2*pi)))
{
printf("Diego Javier Zea\n");
}