[MMTK] problems with reading in protein peptide chains

Konrad Hinsen hinsen@cnrs-orleans.fr
Fri, 6 Dec 2002 10:07:10 +0100


> Traceback (most recent call last):
>   File "align.py", line 12, in ?
>     model='no_hydrogens', c_terminus = 0, n_terminus = 0)
> 
> ...[SNIP]...
> 
> line 298, in setResidueConfiguration
>     raise IOError, 'Atom '+atom.name+' of PDB residue ' + \
> IOError: Atom 1HD1 of PDB residue ILE not found in residue Ile of object
> .Ile1
> 
> Any ideas?

The reason is that you construct a model with no hydrogen atoms,
so obviously the atom 1HD1 cannot be found in it. The easiest
solution is to remove all hydrogen atoms from the PDBConfiguration
before constructing the PeptideChain:

  for chain in configuration2:
      for residue in chain:
	  residue.deleteHydrogens() 

Konrad.               
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