[phenixbb] ls_wunit_k1

[Jianghai Zhu]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070325/8a3f6f1b/attachment-0004.htm>