[Biopython-dev] Error on Bio.PDB

[Diego Zea]

Excuse me, there is not error. Only a warning on a lot of PDBs. I confuse the chain on my example :/


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




>________________________________
> De: Diego Zea <diego_zea at yahoo.com.ar>
>Para: "biopython-dev at biopython.org" <biopython-dev at biopython.org> 
>Enviado: viernes, 28 de diciembre de 2012 20:33
>Asunto: [Biopython-dev] Error on Bio.PDB
> 
>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  
>
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>if ((dx*dp)>=(h/(2*pi)))
>{
>printf("Diego Javier Zea\n");
>}
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