[phenixbb] ls_wunit_k1

Petrus H Zwart PHZwart at lbl.gov
Mon Mar 26 08:42:52 PDT 2007


I guess that development time is a factor that one should take into consideration when seeing these issues. The phenix release that we currently have is still alpha !
The program is not as mature as other refinement programs, but gives good results across the board. phenix is still a work in progress...
P





----- Original Message ----- 
From: Jianghai Zhu <jzhu at cbr.med.harvard.edu> 
Date: Monday, March 26, 2007 6:14 am 
Subject: Re: [phenixbb] ls_wunit_k1 
To: PHENIX user mailing list <phenixbb at phenix-online.org> 

> I found the "automatic adjustment" in my log file.  It says that 
> the  
> target for bulk solvent correction and scaling is changed to  
> ls_wunit_k1 and is required for the target mlhl.  Why is that?  
> for  
> stability issues? 
> 
> 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 26, 2007, at 12:41 AM, Ralf W. Grosse-Kunstleve wrote: 
> 
> >> All right.  The target for my TLS is also LS.  Is that 
> intentional  
> >> too? 
> > 
> > Pavel, who wrote the TLS code, is current offline. 
> > 
> > I don't know if Pavel ran systematic tests to determine the default 
> > target for TLS. 
> > 
> > A couple of months ago I ran systematic tests exercising rigid body 
> > refinement using both the LS and ML targets. Overall it turned 
> out  
> > that 
> > ML is slightly better than LS. For an individual structure and a 
> > particular starting point it can be the other way around, but 
> averaged> over about 70 structures with 100 random starting points 
> each ML 
> > generally outperforms LS. We should have updated the default 
> > accordingly, but it fell through the cracks. 
> > 
> > If you have the time to try out both ML and LS in the refinement of 
> > your structure, we'd be interested to know the results. 
> > 
> > Ralf 
> > 
> > P.S.: What's the version of phenix.refine you are using? -- I'm 
> still> puzzled why you didn't get the "automatic adjustment" messages. 
> > _______________________________________________ 
> > 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/20070326/edc0d55d/attachment-0004.htm>


More information about the phenixbb mailing list