[phenixbb] all reflections are equal, but some more than others

Ed Pozharski epozh001 at umaryland.edu
Tue May 18 10:33:05 PDT 2010

On Mon, 2010-05-17 at 16:20 -0700, Peter Zwart wrote:
> You make it sound like it is a bad thing. The effect of restraint
> weights (ADP, geometry) has most likely a much bigger impact on the
> final structure then a small fraction of smallish intensities (*)


I think discarding data has to be justified.  Two points:

1.  The fraction of negative intensities is not necessarily small.  It
depends on resolution cutoff (and you make an excellent point about
PTS), but looking at scalepack log-files I can tell that in my hands the
fraction is often 10% or more (DISCLAIMER: I belong to I/sigma=1
resolution cutoff cult).

2.  Just because these reflections are weak does not mean that they are
insignificant.  Their contribution to the maps may be small (now I fear
another round of "fill-in missing Fobs with Fc for map calculation"
discussion), but keeping Fc close to zero for these reflections during
refinement seems to be just as important as to keep Fc close to whatever
values the strong reflections have.

The weak reflections are not fundamentally worse than strong(er)
reflections in the same resolution range.  They are measured with
roughly the same precision.  Moreover, the practice of setting negative
intensities to zero and then ignoring them in refinement discards those
that are barely negative and leaves in those that were (quite randomly)
barely positive.

You are absolutely right that other factors will have impact on the
model.  But that does not mean that discarding weak data is justified.
Crystallographic refinement is a Rube Goldberg machine, and all the
components should be as good as we can make them.  Perhaps there could
be something better than French&Wilson, but discarding negative
intensity reflections is hardly the solution.



PS.  Personally I have no stake in this, since I always use truncate.

"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs

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