Dear ALL when you start you refinment 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 refinment, 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 explaination. TKDawoD ----------------------------------------------------------------------------------------------------REMARK 3 NUMBER OF REFLECTIONS : 47312 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 24389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1673REMARK 3 R VALUE (WORKING SET) : 0.1636REMARK 3 FREE R VALUE : 0.2084REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.21 REMARK 3 FREE R VALUE TEST SET COUNT : 3882------------------------------------------------------------------------------------------------------REMARK 3 NUMBER OF REFLECTIONS : 107005 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 56251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1457REMARK 3 R VALUE (WORKING SET) : 0.15.34REMARK 3 FREE R VALUE : 0.1997REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.51 REMARK 3 FREE R VALUE TEST SET COUNT : 3809-----------------------------------------------------------------------------------------------------NUMBER OF REFLECTIONS : 48150 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 25296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1507REMARK 3 R VALUE (WORKING SET) : 0.1470REMARK 3 FREE R VALUE : 0.1918REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.98 REMARK 3 FREE R VALUE TEST SET COUNT : 3841
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 : 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 TKDawoD
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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Hello, default setting is 10% with max 2000 reflections. As Georg said, 0=Work and 1=Test (free). phenix.refine tries its best to figure out what are "work" and "free" flags, as different programs have different conventions. Unless you changed the default, I think you get more than 2000 flags because Fobs+ and Fobs- are counted as separate reflections (2 reflections), while each one of the two must have the same flag (for example, if Fobs+ is "1" then Fobs- must be "1" too). Pavel On 1/21/15 1:31 PM, Tarek DawoD wrote:
Dear ALL
when you start you refinment 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 refinment, 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 explaination.
TKDawoD
---------------------------------------------------------------------------------------------------- REMARK 3 NUMBER OF REFLECTIONS : 47312 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 24389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1673 REMARK 3 R VALUE (WORKING SET) : 0.1636 REMARK 3 FREE R VALUE : 0.2084 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.21 REMARK 3 FREE R VALUE TEST SET COUNT : 3882 ------------------------------------------------------------------------------------------------------ REMARK 3 NUMBER OF REFLECTIONS : 107005 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 56251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1457 REMARK 3 R VALUE (WORKING SET) : 0.15.34 REMARK 3 FREE R VALUE : 0.1997 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.51 REMARK 3 FREE R VALUE TEST SET COUNT : 3809 ----------------------------------------------------------------------------------------------------- NUMBER OF REFLECTIONS : 48150 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 25296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1507 REMARK 3 R VALUE (WORKING SET) : 0.1470 REMARK 3 FREE R VALUE : 0.1918 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.98 REMARK 3 FREE R VALUE TEST SET COUNT : 3841
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participants (3)
-
Georg Mlynek -
Pavel Afonine -
Tarek DawoD