[phenixbb] Phaser and normal mode analysis

[Randy Read]

Hi,

The normal modes only preserve the geometry for infinitesimal shifts, so larger normal modes shifts will perturb the geometry and introduce clashes.  However, since the lowest modes change the energy slowly, they tend not to introduce problems quickly, so most geometry issues will be relatively minor.  

If you get a molecular replacement solution with a normal modes perturbed model, then you'll want to do some refinement of the model to fix up the geometry and relieve any clashes.

Regards,

Randy Read

On 21 Apr 2010, at 08:11, Francois Berenger wrote:

> Hello,
> 
> If I use Phaser's MR_NMA mode, will it introduce clashes into
> the structure or are they taken care of?
> 
> Regards,
> Francois.
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------
Randy J. Read
Department of Haematology, University of Cambridge
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