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? Thanks! Pavel.