[phenixbb] low resolution secondary structure refinement

Nathaniel Echols nechols at lbl.gov
Wed Apr 7 16:54:50 PDT 2010

On Wed, Apr 7, 2010 at 4:48 PM, Pavel Afonine <PAfonine at lbl.gov> wrote:

> rigid body refinement does not employ any restraints. You can use secondary
> structure restraints in refinement of individual coordinates.
> Actually, you can use secondary structure restraints in constrained rigid
> body refinement (SA in torsion angle space).

I'm not sure to what extent this is true.  Ralf, what would be the effect of
those extra H-bonds when running torsion angle dynamics?  Will they be used
in the rigidity analysis, or will they just behave as they would in
cartesian dynamics?

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