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

Pavel Afonine PAfonine at lbl.gov
Fri Dec 4 09:17:13 PST 2009

Hi Joe,

>  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).

When it comes down to refinement, it's impractical to hope to find out 
where the data come from. Sorry for my ignorance in this question.... 
But could you please tell us what are the exact benefits of using Fobs=0 
in refinement, preferable supported by references where it was 
systematically studied. I'm sure I'm missing or forgot something, but 
fail to get it right now at this time of the evening...

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?


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