[phenixbb] Fw: Rfree % calculation (duplicate)
tkdawod at yahoo.com
Wed Jan 21 14:05:37 PST 2015
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 : 47312number of reflections (non-anomalous): 24389R value (working set): 0.1673free R value : 0.2084
free r value test set size (%): 8.21free R value test set count : 3882
number of reflection : 107005number of reflections (non-anomalous): 56251R value (working set):0.1534 free R value : 0.1997free r value test set size (%): 3.51free R value test set count : 3809
number of reflection : 48150number of reflections (non-anomalous): 25296R value (working set): 0.1470free R value : 0.1918free r value test set size (%): 7.98free R value test set count : 3841
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