[phenixbb] number of cycles

Jeff Headd jjheadd at lbl.gov
Tue Mar 1 20:06:56 PST 2011

Hi Keitaro,

> Are B-factors taken into account if both orientations don't clash?
> This is the function of Coot to detect flip.
> I think it's nice if it is automatically done... already implemented?

At present B-factors are only taken into account for waters. Water
molecules with B-factor > 40.0 are ignored from the clash
calculations. Otherwise, all heavy atoms are included. Phenix uses the
Reduce program, which is the same method used by MolProbity.

That is an interesting idea for extending N/Q/H correction, I will
definitely give it some thought and have a look at what Coot is doing.



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