[MMTK] newby: protein to c_alpha

hinsen at llb.saclay.cea.fr hinsen at llb.saclay.cea.fr
Fri Oct 15 12:48:00 CEST 2004

On Oct 15, 2004, at 7:44, mmtk-bounces at python.net wrote:

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> I'm trying to superimpose structurally similar
> proteins with different sequences.  Can this be done
> using the approach in the example analysis.py except
> using only C alphas?  That is, apply the configuration
> of one to the other and then find the transformation
> back to the original.  I have the impression that it
> can but I can't figure out how to generate the c_alpha
> only configuration which I can then apply to the
> moving protein.  Is there a better approach?  Any help
> would be appreciated.
I would do exactly what you propose: do the superposition on the basis 
of the C-alpha atoms.

Constructing a C-alpha model is simple enough, just add

	model = 'calpha'

to the PeptideChain or Protein constructor. The tricky part is ignoring 
the sequence information, because even a C-alpha model still has a 
primary sequence and MMTK will refuse configurations that don't match 
it. The simplest solution is to discard the sequence information right 
from the start by mutating all residues to glycine.

I have made a C-alpha version of the example "analysis.py" which will 
be in the next release. It is also attached for immediate inspiration.

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: hinsen at llb.saclay.cea.fr
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