Re: [phenixbb] mlhl refinement

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 modification. 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? Florian 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

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On Mon, Sep 27, 2010 at 2:32 PM, Florian Schmitzberger wrote:

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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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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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