[phenixbb] Are sigma cutoffs for R-free reflections cheating?
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
A non-default option to include this data would be desirable
(reprocessing it with TRUNCATE YES being even more desirable).
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?
> phenixbb mailing list
> phenixbb at phenix-online.org
More information about the phenixbb