[phenixbb] phenix.refine is renaming experimental phase labels and the purpose of _refine_data.mtz?

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Sat Sep 3 15:21:44 PDT 2011

Hi Francis,

Also it's not desirable to create a _refine_data.mtz as it's unclear where
> the experimental phase labels came from the first place. Suppose I'm doing
> iterative rounds of MRSAD (with updated models during model building),  I
> may have several AutoSol directories containing MRSAD runs for updated
> models.
>  How am I going to know where the HL's in *_refine_data.mtz came from?
>  (grepping .def files?)

The full file names should be in the .eff file.
It may be useful to somehow store them in the mtz file, too. I'll keep it in

> It would be easier if the .def's contained the full paths of the original
>  .mtz files and not a phenix combined data file.  I may have my original
> reflections in one mtz, an R-free set in another, experimental phases in
> another, etc.

That's exactly why I decided to consolidate all inputs in one central file.
In addition, you need some place to store newly generated R-free flags.

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