[phenixbb] Are sigma cutoffs for R-free reflections cheating?
PAfonine at lbl.gov
Fri Dec 4 09:17:13 PST 2009
> 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?
More information about the phenixbb