[phenixbb] ls_wunit_k1

Jianghai Zhu jzhu at cbr.med.harvard.edu
Mon Mar 26 09:02:44 PDT 2007


I consider you guys have done an excellent job.  I am just curious  
for the things happened during my refinement.

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 11:42 AM, Petrus H Zwart wrote:

> 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
> >
> >
>
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