Re: [phenixbb] ls_wunit_k1

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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