[phenixbb] Are sigma cutoffs for R-free reflections cheating?
Joe Krahn
krahn at niehs.nih.gov
Wed Dec 2 15:26:27 PST 2009
Using a sigma cutoff in refinement is almost always a bad idea. It
appears that some people still use them. The problem is that sigma
cutoffs almost always improve R-factors, because it increases the
denominator in the error/average equation. Some people incorrectly think
that the reduced R-factor means that the cutoff was an improvement in
the structure quality.
The result of a sigma cutoff is that the R-factor can be made to look
better than it really is. I think that this should be prevented by never
excluding any R-free reflections by any sort of cutoff criteria. That
keeps the R-free value unbiased. If culling R-free is required for
proper error analysis, or just because the culled data are almost
certainly bogus values, then the un-culled R-free could be a separate value.
Now days, most people use a sigma cutoff of zero, so it is normally not
a big problem. However, it appears that PHENIX still throws out many
reflections where Fobs==0, which can be a significant fraction in the
last shell with anisotropic data. Unfortunately, the exclusion of weak
reflections depends on how amplitudes were derived. If using CCP4
Truncate, those weak reflections will be inflated a bit to a non-zero
value, and a zero-sigma cutoff will have a significantly different
affect. Therefore, I think that the default should be to use reflections
with Fobs==0, with SigFobs > 0 as the criterion for non-absent
reflections in reflection files without a missing number flag (i.e. CNS
format).
Joe Krahn
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