Hi Yusuf, yes, you can request a desired fraction of 'test' reflections to be generated (xray_data.r_free_flags.fraction=) and you can set up an upper limit for the number of 'test' reflections. The defaults are 0.1 and 2000, if I remember correctly, and as far as I know they are good in most of cases. The free-R flags should be evenly distributed over the whole resolution range and each "narrow enough" resolution bin should contain not less than 50 'test' reflections so the ML estimates of distribution parameters (alpha/beta or sigmaa) are reliable. The default in phenix.refine is set up to 140 'test' reflections per bin which is found by systematic search. I can imagine that one needs to lower these values if there are too few data available so setting even a small fraction of reflections aside may be critical. I hope this is not your case at 3A resolution and 12680 reflections! Pavel. On 2/27/09 11:58 AM, Yusuf Akhter wrote:
Hi Everybody!
I am using phenix version 1.3b for refining a structure at 3 A resolution and total number of total reflections are 12680.
I have seen a provision in phenix to change the default maximal number of test flags to be generated and the fraction with this command line
xray_data.r_free_flags.fraction=0.05 xray_data.r_free_flags.max_free=500
My queries are
1)when should somebody use this utility ?? 2)what is minimum number of Rfree flags one should use on this resolution and this total number of reflections??
Any kind of suggestions will be appreciated.
Cheers! Yusuf
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