[phenixbb] NCS constraints in phenix

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Jun 30 09:29:21 PDT 2010

Hi Kenneth,

> If I set the coordinate_sigma in de .def file to zero will this result
> in constrained NCS-refinement?

No, sorry, we don't have "strict NCS" in phenix.refine.
It is on the list of things to do in the next grant cycle.

Some background: phenix.refine uses gradient-driven local minimization,
which minimizes a sum of a penalty terms of the form weight * penalty.
Examples of "penalty" are (f-obs - f-calc)**2 or (distance_ideal -
distance_model)**2, or differences between NCS-related coordinates.
weight = 1 / sigma**2, so if sigma is zero you have a divistion by
zero. Therefore we use sigma=0 as a flag to turn off the corresponding
penalty term.
A constraint system is generally much more complicated than a
restraint system.


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