[phenixbb] [phenix] generate r free flags in phenix.refine not obeying high resolution limit?

Pavel Afonine PAfonine at lbl.gov
Wed Aug 20 12:47:33 PDT 2008

Here is the paper where I hope these questions are answered:
Acta Cryst. (1995). A51, 880-887

Also, the implementation of ML target calculation and other relevant 
calculations in phenix.refine are done exactly as described in this paper.

Namely, the ML target in phenix.refine is the formula 14 in the above 
paper; and the estimation of distribution parameters alpha&beta is 
described in Appendix

phenix.refine is smart about generating the good free-R flags, where all 
necessary considerations are taken into account. Twinning, if present, 
is taken care of too.


On 8/20/2008 12:12 PM, Pascal EGEA wrote:
> Hi All,
> Following Pavel's answer to Francis Reyes, I have a very basic  
> question about this too.
> What is a good distribution of reflections and what are thin bins of  
> resolution to ensure correct ML estimations?
> Are there any basic statistical rules that should be considered.
> Thanks
> Pascal
> Pascal F. Egea, PhD
> Post Doctoral Researcher
> University of California San Francisco
> Department of Biophysics and Biochemistry
> Robert Stroud Laboratory
> pascal at msg.ucsf.edu
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