[phenixbb] Are sigma cutoffs for R-free reflections cheating?

Ed Pozharski epozh001 at umaryland.edu
Fri Dec 4 10:08:52 PST 2009

AFAIU, Joe is referring to the situation where negative intensities are
converted to FOBS=0.  Ignoring them would allow refinement to have any
FCALC for these reflections when in fact we do have some information
about them.  I am not aware of any systematic study of this question,
but it *seems* rather obvious that ignoring zero reflections is a wrong
thing to do *in these circumstances*.

Of course, none of this is a problem when negative intensity reflections
are processed by truncate to have positive FOBS according to their
sigmas, since it is then virtually impossible to have FOBS exactly zero.
So I would say that the problem is not phenix.refine, but the I->F
conversion protocol which assigns zero values to reflections which are
actually not zero.

> Imagine I have a dataset of resolution 26.0-2.3A. Do you really think it 
> would be great to do refinement in resolution say 100.0-0.25A, where all 
> missing Fobs are zeros?

No, it won't be great but I don't think Joe or anyone else is suggesting
that.  If I understand correctly, he is saying that it might be a good
idea not to ignore 25% of reflections in the highest resolution shell
that had negative intensities (that is if I choose not to use
French&Wilson, which would be my fault).




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