[MMTK] replaceResidue

Konrad Hinsen research at khinsen.fastmail.net
Thu Jun 16 07:04:13 UTC 2011


On 15 Jun 2011, at 00:14, Talipov, Marat wrote:

> My idea is to store the residue coordinates in a Z-matrix format in  
> the database and use them
> to calculate the Cartesian coordinates using positions of the  
> backbone atoms (say, CA,C,N) as a reference.
>
> However, I'm not sure what is the best place to keep Z-matrix  
> coordinates of residues. I thought about XXX_sidechain file, but I  
> got an error "name 'ZMatrix' is not defined".

That's easy to fix: add the line

	from MMTK.ConfigIO import ZMatrix

to your XXX_sidechain file. Those files are in fact Python scripts  
which are executed after an implicit "from MMTK.GroupEnvironment  
import *". MMTK.GroupEnvironment does not contain ZMatrix  
(MMTK.MoleculeEnvironment does), so that's why you need to add the  
import yourself.

Note that a ZMatrix is not the only solution, you could go for  
Cartesian coordinates and apply translations/rotations to the template  
coordinates to align the sidechain with the backbone it is being  
grafted on. I am not sure what the best way is, assuming there is one.

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: research at  khinsen dot fastmail dot net
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