Petrus H Zwart
PHZwart at lbl.gov
Sun Mar 25 17:18:12 PDT 2007
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.
----- Original Message -----
From: Jianghai Zhu <jzhu at cbr.med.harvard.edu>
Date: Sunday, March 25, 2007 2:58 pm
Subject: [phenixbb] ls_wunit_k1
To: PHENIX user mailing list <phenixbb at phenix-online.org>
> I happen to notice that the target function of "Bulk solvent
> correction and scaling" in a phenix.refine run is ls_wunit_k1.
> 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
> use the ML function or something bad will happen?
> 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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