[phenixbb] Geometry Restraints - Anisotropic truncation
det102 at uoxray.uoregon.edu
Thu May 3 10:43:44 PDT 2012
Yes, "never" is too big a word for this, but writing "nearly never" simply
begs for explanation. The rejection test that Pavel and Randy perform is
extremely conservative and individualistic. In addition, the last time I
looked in a Phaser log file the excluded reflections were individually listed
and, as you said, the exile is not permanent - there is a parole hearing
every round of the calculation.
This is very different than the mass rejections being discussed here.
On 05/03/12 10:23, Nathaniel Echols wrote:
> On Thu, May 3, 2012 at 10:05 AM, Dale Tronrud <det102 at uoxray.uoregon.edu> wrote:
>> An important point is that the Fc's must never be used to judge the
>> quality of the Fo's in a production environment.
> I'm not sure that's completely fair - they can certainly be used to
> identify Fobs values that are wildly at odds with expectations. This
> is what Pavel does with outlier rejection in phenix.refine (I forget
> the exact reference for this protocol but I think it's Read 1999 or
> something like that). The difference, I think, is one of degree, and
> also that (at least in the current version) the outliers are
> recalculated at each cycle of refinement and never permanently
> excluded, unlike anisotropic truncation.
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