[MMTK] superimposing a tetramer

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu May 29 08:32:35 UTC 2008


On 28.05.2008, at 13:10, Ramon Crehuet wrote:

> I am trying to superimpose the C_alphas of two tetrameric proteins.  
> I am trying to follow the example script, but the lines
> tetramer_1 = configuration2.peptide_chains[0]should be changed to  
> something like:
> tetramer = configuration2.peptide_chains but then, tetramer is a  
> list and functions like
> PeptideChain(tetramer, model='calpha')
>
> cannot be directly applied. Of course, I could use map, etc, but I  
> was wondering if there is a simpler way.

That depends on what exactly you have and what exactly you want to  
do. Do you have two different configurations (for example two PDB  
files) for the same tetrameric protein? In that case, you can just do  
something like

universe = InfiniteUniverse()
universe.protein = Protein('conf1.pdb', model='calpha')
conf1 = universe.copyConfiguration()
PDBConfiguration('conf2.pdb').applyTo(universe.protein)

transformation, rms = universe.protein.findTransformation(conf1)
universe.protein.applyTransformation(transformation)

Konrad.
--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr
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