[phenixbb] Fw: Rfree % calculation (duplicate)

Georg Mlynek georg.mlynek at univie.ac.at
Thu Jan 22 08:17:37 PST 2015


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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