<BODY contentEditable=true onload=parent.init()><P>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 !</P>
<P>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>
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<P><BR><BR>----- Original Message ----- <BR>From: Jianghai Zhu <jzhu@cbr.med.harvard.edu> <BR>Date: Monday, March 26, 2007 6:14 am <BR>Subject: Re: [phenixbb] ls_wunit_k1 <BR>To: PHENIX user mailing list <phenixbb@phenix-online.org> <BR><BR>> I found the "automatic adjustment" in my log file. It says that <BR>> the <BR>> target for bulk solvent correction and scaling is changed to <BR>> ls_wunit_k1 and is required for the target mlhl. Why is that? <BR>> for <BR>> stability issues? <BR>> <BR>> Jianghai <BR>> <BR>> +++++++++++++++++++++++++++++++ <BR>> Jianghai Zhu, Ph.D <BR>> CBR Institute for Biomedical Research <BR>> Department of Pathology <BR>> Harvard Medical School <BR>> 200 Longwood Ave., Boston, MA 02115 <BR>> Ph: 617-278-3211 <BR>> Fx: 618-278-3232 <BR>> +++++++++++++++++++++++++++++++ <BR>> <BR>> <BR>> <BR>
> On Mar 26, 2007, at 12:41 AM, Ralf W. Grosse-Kunstleve wrote: <BR>> <BR>> >> All right. The target for my TLS is also LS. Is that <BR>> intentional <BR>> >> too? <BR>> > <BR>> > Pavel, who wrote the TLS code, is current offline. <BR>> > <BR>> > I don't know if Pavel ran systematic tests to determine the default <BR>> > target for TLS. <BR>> > <BR>> > A couple of months ago I ran systematic tests exercising rigid body <BR>> > refinement using both the LS and ML targets. Overall it turned <BR>> out <BR>> > that <BR>> > ML is slightly better than LS. For an individual structure and a <BR>> > particular starting point it can be the other way around, but <BR>> averaged> over about 70 structures with 100 random starting points <BR>> each ML <BR>> > generally outperforms LS. We should have updated the default <BR>
> > accordingly, but it fell through the cracks. <BR>> > <BR>> > If you have the time to try out both ML and LS in the refinement of <BR>> > your structure, we'd be interested to know the results. <BR>> > <BR>> > Ralf <BR>> > <BR>> > P.S.: What's the version of phenix.refine you are using? -- I'm <BR>> still> puzzled why you didn't get the "automatic adjustment" messages. <BR>> > _______________________________________________ <BR>> > phenixbb mailing list <BR>> > phenixbb@phenix-online.org <BR>> > http://www.phenix-online.org/mailman/listinfo/phenixbb <BR>> <BR>> </P></BODY>