[MMTK] Metalloprotein

khinsen at cea.fr khinsen at cea.fr
Mon Aug 1 16:45:54 CEST 2005

On Jul 26, 2005, at 6:09, Raúl Mera wrote:

> peptidechain class. My problem is that I can't build a
> protein with that peptide because when I try to buld
> one with
> protein=Protein(chain)

The Protein constructor expects a *list* of chains, so you should do

	protein = Protein([chain])

> I get this error:
>   File "./load_prot.py", line 35, in ?
>     sod1_p=Protein(sod1)
>   File
> "/usr/lib/python2.3/site-packages/MMTK/Proteins.py",
> line 597, in __init__
>     ss = self._findSSBridges(molecules)
>   File
> "/usr/lib/python2.3/site-packages/MMTK/Proteins.py",
> line 730, in _findSSBridges
>     cys = cys + m.residuesOfType('cys') +
> m.residuesOfType('cyx')
>   File
> "/usr/lib/python2.3/site-packages/MMTK/Biopolymers.py",
> line 100, in residuesOfType
>     if string.lower(r.type.symbol) in types:
> AttributeError: 'NoneType' object has no attribute
> 'symbol'

Right, the Protein constructor supposes that all groups in the 
PeptideChain object are residues. Your Zinc group isn't, which causes 
the error. There is more code that makes the same assumption, so 
addGroup on the chain does not look like a good approach.

> I tried to build the protein and then add the metal
> with addGroup(), but when I use
> protein[0].addGroup(...) I get this problem:
> "/usr/lib/python2.3/site-packages/MMTK/ChemicalObjects.py",
> line 767, in addGroup
>     raise ValueError, "bond %s-%s outside object" % \
> ValueError: bond AtomCluster ZN-Atom
> ..chain0.His63.sidechain.N_delta_1 outside object

Because the Zinc atom is not part of the protein.

Try the following:

	protein = Protein([chain, zinc_group])

That makes the zinc part of the protein object before adding it to the 
peptide chain. I don't promise that this will work, because I never 
tested it, but it should work, so if it doesn't, I'll do my best to fix 
MMTK until it does.

Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr

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