[phenixbb] mlhl refinement

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Sep 27 18:49:43 PDT 2010

Hi Nat and Florian,

Yes, the overall_best_denmod_map_coeffs.mtz file is really intended only
for drawing maps.  Normally this file has no HL coefficients in it (they
are all zero).  In cases where they do have HL coeffs (obtained with
hl=True) these HL coeffs are after density modification.

As Nat suggests, it is best to use exptl_fobs_phases_freeR_flags.mtz for
refinement. It contains experimental amplitudes and HL coeffs from
experimental phasing only.

All the best,
Tom T

 >> On Mon, Sep 27, 2010 at 2:32 PM, Florian Schmitzberger
>> <schmitzberger at crystal.harvard.edu> wrote:
>>> I am running Phenix version 1.6.4.-486 on imac. I just wanted to refine
>>> (phenix.refine) a model with MLHL target and experimental phase
>>> information.
>>> Strange thing is when I load the mtz file, as written out from Phenix
>>> Autosol (overall_best_denmod_map_coeffs.mtz) into the GUI, the Phenix
>>> refine
>>> GUI does not seem to any phase information. Only picks up FP and SIGFP
>>> labels; but not the Hendrickson-Lattman coefficients, which are present.
>>> The
>>> following message comes up when I try to chose mlhl refinement: " You
>>> have
>>> selected 'mlhl' as the refinement target, but no experimental phases
>>> were
>>> supplied. If you wish to use phase restraints in refinement, please add
>>> or
>>> select experimental phases, or choose another target function". I guess
>>> it
>>> is not such a major problem as I can save the .eff file and manually
>>> edit it
>>> to include the HL coefficients and then run Phenix (as long as Phenix
>>> then
>>> recognizes them from the mtz file).
>> You probably shouldn't be using that file for refinement - instead,
>> use the one labeled "exptl_fobs_phases_freeR_flags_X.mtz" (X will be
>> some integer corresponding to the solution number), which has R-free
>> flags used for building.  I'm not sure where the HL coefficients in
>> overall_best_denmod_map_coeffs.mtz are coming from, although they may
>> be identical to what's in the exptl_fobs file (Tom can clarify).
>> That said, I couldn't reproduce the problem here - what other files
>> did you load at the same time, and in which order?
>> thanks,
>> Nat
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