[phenixbb] ls_wunit_k1

Petrus H Zwart PHZwart at lbl.gov
Sun Mar 25 19:06:49 PDT 2007


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 <jzhu at cbr.med.harvard.edu> 
Date: Sunday, March 25, 2007 5:18 pm 
Subject: Re: [phenixbb] ls_wunit_k1 
To: PHENIX user mailing list <phenixbb at phenix-online.org> 

> 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 <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> 
> > 
> > > 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 
> > phenixbb at phenix-online.org 
> > http://www.phenix-online.org/mailman/listinfo/phenixbb 
> 
> 
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