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

Nathaniel Echols nechols at lbl.gov
Sat Sep 3 14:10:27 PDT 2011

On Sat, Sep 3, 2011 at 1:25 PM, Francis E Reyes
<Francis.Reyes at colorado.edu> wrote:
> 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).

Phenix doesn't really track column labels internally, or propagate
them - it sees Hendrickson-Lattman coefficients, and automatically
labels them HL*.  The method that handles this isn't even capable of
handling "HLAM" without modifying the code - the "A" will always end
up at the end.  Actually, Phenix doesn't organize data in "columns"
either, so it's pretty detached from MTZ format.

I'm not sure what the distinction between HLA and HLAM is - your
interpretation sounds correct, but that would mean that AutoSol is
writing out the density-modified phases instead of the experimental
phases.  Which doesn't sound right to me; I guess you could use
phaser_1.mtz to be safe.


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