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 <[email protected]>
Date: Sunday, March 25, 2007 5:18 pm
Subject: Re: [phenixbb] ls_wunit_k1
To: PHENIX user mailing list <[email protected]>

> 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 <[email protected]>
> > Date: Sunday, March 25, 2007 2:58 pm
> > Subject: [phenixbb] ls_wunit_k1
> > To: PHENIX user mailing list <[email protected]>
> >
> > > 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
> > > +++++++++++++++++++++++++++++++
> > >
> > >
> > >
> > >
> >
> > _______________________________________________
> > phenixbb mailing list
> > [email protected]
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>