[MMTK] Creating a Protein object from one chain of the PDB

Konrad Hinsen konrad.hinsen at cea.fr
Thu Mar 16 17:26:43 CET 2006

On Mar 16, 2006, at 16:56, vanitha at cs.wisc.edu wrote:

> Thanks again. Also, is it possible to apply the minimizer to just  
> one of
> the many proteins I added to the universe?

The minimizer always acts on the whole universe, because that's what  
the energy is defined for. However, you can fix the atoms of all but  
one protein, such that only one protein is affected by the  
minimization. Just do

	for atom in protein1:
		atom.fixed = True

And don't forget to set this to "False" (or to do del atom.fixed)  
when you do want to move those atoms - the "fixed" attribute is also  
used by MD integrators.

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: konrad.hinsen at cea.fr

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