[phenixbb] mlhl refinement

Florian Schmitzberger schmitzberger at crystal.harvard.edu
Tue Sep 28 06:58:37 PDT 2010

Hi Tom and Nat,

I started the Autosol with selenium sites found by ShelxD. So no  
substructure search was carried out; just phasing and density  

In this case I don't see a file exptl_fobs_phases_freeR_flags.mtz  
produced anywhere in the directory (and also not in TEMP0).  The mtz  
files I see being written out are: F_ano.; phaser, resolve and then  
overall_best_denmod_map_coefficients (overall_denmod_map_coefficients  
does also not have the assigned R_free flag anymore).

So I am confused. Which mtz should I use then?


On Sep 27, 2010, at 9:49 PM, Thomas C. Terwilliger wrote:

> 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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Florian Schmitzberger
Biological Chemistry and Molecular Pharmacology
Harvard Medical School
250 Longwood Avenue, SGM 130
Boston, MA 02115, US
Tel: 001 617 432 5602

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