[phenixbb] test set count question
pafonine at lbl.gov
Wed Aug 8 11:19:28 PDT 2012
> 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
it's best to work with unmanipulated original data, which is Fobs(+) and
<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
Although I doubt it would make any visible effect on final refined
> 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
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,
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