[phenixbb] ls_wunit_k1

Petrus H Zwart PHZwart at lbl.gov
Sun Mar 25 20:29:44 PDT 2007


I have seen that as well, not sure why that is. I guess it has to do with stability issues. Not sure if you can enforce the use of an ML target there.
Peter



----- Original Message ----- 
From: Jianghai Zhu <jzhu at cbr.med.harvard.edu> 
Date: Sunday, March 25, 2007 7:14 pm 
Subject: Re: [phenixbb] ls_wunit_k1 
To: PHENIX user mailing list <phenixbb at phenix-online.org> 

> All right.  The target for my TLS is also LS.  Is that intentional 
> too? 
> 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 10:55 PM, Petrus H Zwart wrote: 
> 
> > 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 
> > > 
> > > 
> > 
> > _______________________________________________ 
> > 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/20070325/6074402c/attachment-0004.htm>


More information about the phenixbb mailing list