[phenixbb] Appropriate number of reflections for FreeR
berrye at upstate.edu
Sun Nov 3 03:50:25 PST 2013
Looking at it from the other side- suppose we say for a robust refinement we need a certain number of reflections- say 4 times the number of atoms, maybe less, I don't know. Any more than that is not really going to affect the structure, So if you have high resolution you can afford to use a large percentage of free reflections, and the cross-validation and maximum liklihood will go really well, even with thin shells. On the other hand at low resolution, well, sorry, you really can't spare any reflections for cross-validation. (I have no idea whether this makes sense or not, but it would be another way of looking at it).
>>> Mark van Raaij 11/01/13 7:39 PM >>>
the limit of 2000 reflections I guess is just because it would be a waste to "throw away" more reflections for refinement, once the statistical minima for calculating a reliable Rfree have been met. I.e. if you have 100.000 reflections, it would be a waste to use 5 or 10% of the reflections instead of just 2%. I'd rather use as many as possible reflections for refinement.
On 31 Oct 2013, at 20:21, Pavel Afonine wrote:
> Hi Joe,
> flags should be selected such that there is enough of them in each relatively thin resolution shell (thin enough so ML target parameters can be considered constant in each such shell). Lower end is about 50 reflections per shell. All in all this usually translates into about 10% overall.
> Yes, there is a limit parameter set to 2000 by default. I don't know what's the rationale for having it, may be someone can explain.
> On 10/31/13 12:10 PM, Joseph Noel wrote:
>> Hi All. I think I have asked this before but forgot. Old age. What is
>> the appropriate number / percentage of reflections to flag for a
>> statistically appropriate Free-R calculation? If I am correct, the
>> reflection file editor in Phenix chooses by default either 10% of the
>> measured reflections or 2000 whichever comes first.
>> Joseph P. Noel, Ph.D.
>> Arthur and Julie Woodrow Chair
>> Investigator, Howard Hughes Medical Institute
>> Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
>> The Salk Institute for Biological Studies
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