[phenixbb] Table 1 stastics

Nathaniel Echols nechols at lbl.gov
Thu Oct 25 12:09:49 PDT 2012

On Thu, Oct 25, 2012 at 12:03 PM, Kip Guja <kip at pharm.stonybrook.edu> wrote:
> I apologize if this is way off base, but perhaps the difference in completeness is due to the (potential) difference between I-obs / F-obs (original reflections after data processing and reduction) and I-obs-filtered / F-obs-filtered (reflections actually used in refinement).
> Specifically, I am referring to data that was refined in older versions of Phenix (before French&Wison was default) -- and datasets that have some amount of weak reflections or negative intensities. Perhaps that is the case here?

Definitely possible - and there are probably still other filtering
steps in Phenix that don't use French & Wilson.  Generally the safest
thing to do is either a) run French & Wilson treatment immediately
once you have your data (depending on how you process it this may
happen automatically), or b) always use the original intensities for
everything (which will work for Phenix, more or less, but not other

However, the "filtered" arrays with outliers removed generally won't
be re-used anywhere - they are included for the sake of having a
complete representation of the refinement result, but I believe they
are also ignored (based on the label) by other programs.


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