[phenixbb] test set count question

Filip YABUKARSKI fyabukar at embl.fr
Wed Aug 8 07:24:22 PDT 2012

Dear all,

I am refining a structure with phenix.refine using a .mtz which 
contains F/SigF and DF/SigDF (CCP format from xdsconv) and i have 
something like 10000 unique reflections. The test set was created with 
the uniqueify script. If I understand correctly in the manual it is 
written that phenix.refine will separate the <F>/<SigF> into "F(+) 
SIGF(+) F(-) SIGF(-)), instead of keeping the original non-anomalous 
amplitudes". My question is about the "FREE R VALUE TEST SET COUNT" in 
the .pdb after phenix.refine. If I understand correctly the number for 
the test set will also be "doubled" because the <F> will be separated 
into F+ F-? Logically both F+/F- after separation are kept in the test 
set is this right? And an impair number for the test set in this case 
means that only the F+ OR F- was observed? Sorry if I ask a trivial 
question but I just want to be sure I am using the program in the right 

Thanks in advance

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