Weerd, my source code shows that the default is ml: cd /net/rosie/scratch1/phzwart/CCTBX/Sources/mmtbx/mmtbx/bulk_solvent/ more bulk_solvent_and_scaling.py master_params = iotbx.phil.parse("""\ bulk_solvent = True .type = bool anisotropic_scaling = True .type = bool statistical_solvent = False .type = bool k_sol_b_sol_grid_search = True .type = bool minimization_k_sol_b_sol = True .type = bool minimization_b_cart = True .type = bool target = ls_wunit_k1 *ml .type = choice Pavel developed some heuristics governing optimal settings in certain cases which might come into play here. I suspect it might be due to model size, resolution or other factors. If not, I am puzzled. Cheers Peter ----- Original Message ----- From: Jianghai Zhu Date: Sunday, March 25, 2007 5:18 pm Subject: Re: [phenixbb] ls_wunit_k1 To: PHENIX user mailing list

Hi Peter,

You are right. Somehow, the default target function in refinement.bulk_solvent_and_scale is LS, not ML.

Jianghai

+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

On Mar 25, 2007, at 8:18 PM, Petrus H Zwart wrote:

...

Hi Jianghai,

Interesting, I though that by default an ML target is used. Something must have happened somewhere.

Check the parameter file and look for the section on bulk solvent scaling ( refinement.bulk_solvent_and_scale ). A target function

...

can be defined, you have the choice between ml and ls_wunit_k1, ml is (I think) selected by default.

There is also a switch present that triggers the refinement of bulk solvent parameters using a least squares target if the r value is larger than a certain value:

ls_bulk_solvent_and_scale_if_r_greater_then = 0.99

Changing the parameter you propose changes the least squares target type if the main target selected is ls and has (as far as I understand) no influence on bulk solvent scaling. If you want, you can send a log file for a closer look.

HTH

Peter

----- Original Message ----- From: Jianghai Zhu Date: Sunday, March 25, 2007 2:58 pm Subject: [phenixbb] ls_wunit_k1 To: PHENIX user mailing list

...

Hi,

I happen to notice that the target function of "Bulk solvent correction and scaling" in a phenix.refine run is ls_wunit_k1. Does that mean LS function for bulk solvent correction and scaling is the > default in phenix.refine? If I uncheck ls_wunit_k1 in refinement.ls_target_names in my parameter file, will phenix.refine use the ML function or something bad will happen?

...

Jianghai

+++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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