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

Thomas C. Terwilliger terwilliger at lanl.gov
Sat Sep 3 14:47:36 PDT 2011

Hi Francis and Nat,

Unfortunately there already is a little discrepancy in the naming of HL
coeffs.  Resolve does write out HLAM etc as density modified phase
information...However the exptl_fobs_freeR_flags_1.mtz from autosol are
also labeled HLAM even though they are experimental HL coeffs.  I
apologize for the lack of consistency there.

-Tom T

>> 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
>>> 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.
>> -Nat
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