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

Pavel Afonine pafonine at lbl.gov
Wed Aug 20 09:23:07 PDT 2008

Hi Francis,

it is always the best to generate the free R flags for the whole dataset 
and this is what phenix.refine does (I will have to double-check, 
though). Because, for example, if you change your mind and later decide 
to use more data, you will run into trouble with generating free R flags 
for the rest of reflections for which you haven't done it in the beginning.

Also, phenix.refine generates free R that are evenly distributed over 
the resolution, making sure that relatively thin resolution bins receive 
enough of reflections (to assure correct ML estimations).

So, I don't see any problem here... Am I missing something?


On 8/20/2008 8:58 AM, Francis E Reyes wrote:
> Hi all
> When generating R-Free flags from phenix refine, flags are generated  
> all the way to the limit of the data. However, shouldn't flags be  
> generated up to the limit of the data if specified via  
> refinement.input.xray_data.high_resolutio
> n ? If not, are the statistics for R/Rfree matching to high resolution  
> data that may be suspicious ?
> Thanks
> FR
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
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