[MMTK] comparing modes from different universes

Konrad Hinsen hinsen at cnrs-orleans.fr
Mon Nov 26 17:18:56 UTC 2007

On Nov 26, 2007, at 14:25, Edvin Fuglebakk wrote:

> I have superimposed structures with coordinates for the  
> superimposition
> coded in different pdb-files (one file for each structure).
> Can I rely on MMTK to preserve these structures relative  
> orientation to
> each other when loaded into different universes so that the directions
> of the atomic displacements are comparable?

Yes. MMTK takes the coordinates of the atoms from the PDB files  
without modification. If the structures are aligned in the PDB files,  
they will be in the different MMTK universes as well.

> The following test seems to work, but I would like assurance that  
> it is
> a reliable way to do it:
>     #load the structures into different universes
>     uni=InfiniteUniverse(CalphaForceField())
>     uni.s1=Protein(pdbfile1, model='calpha')
>     uni2=InfiniteUniverse(CalphaForceField())
>     uni2.s2=Protein(pdbfile2, model='calpha')

This is fine.

>     #load the structures into the same universe
>     combinedUniverse=InfiniteUniverse(CalphaForceField())
>     combinedUniverse.s1=Protein(pdbfile1, model='calpha')
>     combinedUniverse.s2=Protein(pdbfile2, model='calpha')

This is fine as well, but if you do normal mode calculations, you  
will get bizarre results with overlapping proteins.

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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