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 <[email protected]>
Date: Monday, March 26, 2007 6:14 am
Subject: Re: [phenixbb] ls_wunit_k1
To: PHENIX user mailing list <[email protected]>

> 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
> > [email protected]
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>