[phenixbb] phenix and weak data

Douglas Theobald dtheobald at brandeis.edu
Fri Dec 7 13:54:01 PST 2012

Hi Nat,

On Dec 6, 2012, at 9:36 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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;

Thanks for the clarification. I guess this was part of my question --- even if phenix does not explicitly use exptl sigmas, perhaps the ML weighting is doing more-or-less the same thing by fitting the weights?  

> 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.  

Maybe I've misunderstood, but Karplus and Diederichs used phenix in their paper arguing for including weak data.  Whether the benefit they describe is considered cosmetic or non-trivial, it at least appears that including very weak data doesn't hurt.  At least with phenix.  

> 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.
> -Nat
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