[phenixbb] phenix and weak data

Nathaniel Echols nechols at lbl.gov
Thu Dec 6 18:36:39 PST 2012

On Thu, Dec 6, 2012 at 2:35 PM, Douglas Theobald <dtheobald at brandeis.edu> wrote:
> Many have argued that we should include weak data in refinement --- e.g., reflections much weaker than I/sigI=2 --- in order to take advantage of the useful information found in large numbers of uncertain data points (like argued in the recent Karplus and Diederichs Science paper on CC1/2).  This makes sense to me as long as the uncertainty attached to each HKL is properly accounted for.  However, I was surprised to hear rumors that with phenix "the data are not properly weighted in refinement by incorporating observed sigmas" and such.  I was wondering if the phenix developers could comment on the sanity of including weak data in phenix refinement, and on how phenix handles it.

As a supplement to what Pavel said: yes, phenix.refine does not use
experimental sigmas in the refinement target.  I am very hazy on the
details, but it is not at all clear that this actually matters in
refinement when maximum likelihood weighting is used; if there is a
reference that argues otherwise I would be interested in seeing it.
(I don't know what the least-squares target does - these are
problematic even with experimental sigmas.)

In practice I do not think it will be a problem to use data out to
whatever resolution you feel appropriate - and it may indeed help -
but of course your overall R-factors will be slightly higher, and the
refinement will take much longer.  Having experimented with this
recently, my instinct would be to refine at a "traditional" resolution
cutoff for as long as possible, and add the extra, weak data near the
end.  If I was working at a resolution that were borderline for
automated building, I might be more aggressive.


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