[phenixbb] ls_wunit_k1

Petrus H Zwart PHZwart at lbl.gov
Sun Mar 25 17:18:12 PDT 2007

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.

----- 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 
> +++++++++++++++++++++++++++++++ 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070325/75a35080/attachment-0004.htm>

More information about the phenixbb mailing list