[phenixbb] ls_wunit_k1

Petrus H Zwart PHZwart at lbl.gov
Sun Mar 25 19:55:21 PDT 2007


Yes. 
It is more robust and used in the so called MZ protocol. It has a large radius of convergence.
Peter


----- Original Message ----- 
From: Jianghai Zhu <jzhu at cbr.med.harvard.edu> 
Date: Sunday, March 25, 2007 6:25 pm 
Subject: Re: [phenixbb] ls_wunit_k1 
To: PHENIX user mailing list <phenixbb at phenix-online.org> 

> The default target for rigid body is LS from "phenix.refine --show- 
> 
> defaults=all".  Is this intentional? 
> 
> 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 10:14 PM, Jianghai Zhu wrote: 
> 
> > I checked my log file and didn't find "automatic adjustment".  
> My  
> > main target is mlhl.  However, the target function for rigid 
> body  
> > is ls_wunit_k1.  I didn't choose that.  Is LS the default for 
> rigid  
> > body? 
> > 
> > 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 10:00 PM, Ralf W. Grosse-Kunstleve wrote: 
> > 
> >>> You are right.  Somehow, the default target function in 
> >>> refinement.bulk_solvent_and_scale is LS, not ML. 
> >> 
> >> The default (phenix.refine --show-defaults=all) is actually ml. 
> >> However, if the main target is set to ls the bulk_solvent_and_scale 
> >> target is automatically reset to ls, too. There should be  
> >> corresponding 
> >> messages in the log file ("automatic adjustment"). 
> >> Ralf 
> >> _______________________________________________ 
> >> phenixbb mailing list 
> >> phenixbb at phenix-online.org 
> >> http://www.phenix-online.org/mailman/listinfo/phenixbb 
> > 
> > _______________________________________________ 
> > phenixbb mailing list 
> > phenixbb at phenix-online.org 
> > http://www.phenix-online.org/mailman/listinfo/phenixbb 
> 
> 
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