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

Francis E Reyes Francis.Reyes at Colorado.EDU
Sat Sep 3 13:25:32 PDT 2011

Hi all

When specifying exptl_fobs_phases_freeR_flags_1.mtz (HLAM,HLBM.HLCM,HLDM) as an experimental phase file in phenix.refine via the .def file,  these HL coefficients are written to *_refine_data.mtz as HLA,HLB,HLC,HLD. 

Now forgive me if I'm incorrect but HLA,HLB,HLC,HLD != HLAM,HLBM,HLCM,HLDM ? (where the former should come from phaser_1.mtz and the latter from resolve_1.mtz reflecting the density modification step). 

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?) 

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. 


Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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