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

Phil Jeffrey pjeffrey at princeton.edu
Fri Dec 4 10:06:49 PST 2009

That's not the point, at least not the way I read this.

Weak reflections with Intensity < 0 get set to |F|=0 by CCP4's Truncate 
with the TRUNCATE NO set (in script files, it's called something else in 
CCP4i).  That's not the same as a Missing Reflection.  Ergo the fact 
that F=0 means that it is weak, but with some even larger uncertainty 
than it was measured with, since you don't know how negative I/sigI was. 
  Nevertheless this does contain information as to the ballpark of 
reflection magnitude.

A non-default option to include this data would be desirable 
(reprocessing it with TRUNCATE YES being even more desirable).

Phil Jeffrey

Pavel Afonine wrote:
> 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.
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