Hi Filip,
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".
it's best to work with unmanipulated original data, which is Fobs(+) and Fobs(-). <Fobs> or "F/SigF and DF/SigDF" are derived from Fobs(+) and Fobs(-) with some information lost. That is you cannot restore the original Fobs(+) and Fobs(-) from <Fobs> or from "F/SigF and DF/SigDF". phenix.refine restores Fobs(+) and Fobs(-) from "F/SigF and DF/SigDF" for internal use making an arbitrary decision about the sign. phenix.refine cannot handle "F/SigF and DF/SigDF" and has no reason to do this. Although I doubt it would make any visible effect on final refined structure.
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"
Yes, it's a good idea to put "" around doubled since it's not precisely doubled because of +,- and singleton reflections.
Logically both F+/F- after separation are kept in the test set is this right?
Yes, "+" and "-" reflections have the same test set value, if this is what you mean.
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 way
"+" and "-" are individually measured reflections so I'm not sure why to hide this fact and count them as one reflection... All the best, Pavel