Dear Tarek, not sure if I understood exactly what you wanted to ask. If you open the .mtz using a terminal/commandline with phenix.mtz.dump -c yourmtz.mtz you will see the columns hkl F-obs SIF-obs R-free-flags and in the R-free-flags colum you sometimes see a 0 or a 1. A 1 means that this reflection is flagged/marked as Rfree. A 0 that it is used for refinement. Be aware that other programs might assign different flag values. But when you than continue using phenix refine it is usually clever enough to figure the right flag out. Otherwise you can set the test flag value for phenix.refine in the gui under configure --> input data --> test flag value At the end of the refinement just check in the result tab if #work and #free are logical. Best Georg. On 01/21/2015 11:05 PM, Tarek DawoD wrote:
Dear ALL
when you start you refinement in phenix with ***.sca file, fraction of reflection in test set will be created. under *options *(bottom) in phenix refine, you could see that fraction of reflection in test set is 0.1 which means 10 % by looking to the PDB header for completely different structures (below) you will find different percentage but always FREE R VALUE TEST SET COUNT is around 3800. so it always take the same 3800 count regardless the number of reflections.
When you look in generated mtz file after the refinement, you see under R-free-flags(+) and R-free-flags(-) either 0 or 1. what does 0 or 1 mean?
Thank you in advance for explanation.
number of reflection : 47312 number of reflections (non-anomalous): 24389 R value (working set): 0.1673 free R value : 0.2084 free r value test set size (%): 8.21 free R value test set count : 3882
number of reflection : 107005 number of reflections (non-anomalous): 56251 R value (working set):0.1534 free R value : 0.1997 free r value test set size (%): 3.51 free R value test set count : 3809
number of reflection : 48150 number of reflections (non-anomalous): 25296 R value (working set): 0.1470 free R value : 0.1918 free r value test set size (%): 7.98 free R value test set count : 3841
TKDawoD
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