[phenixbb] mlhl refinement

Nathaniel Echols nechols at lbl.gov
Mon Sep 27 14:47:32 PDT 2010

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?


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