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

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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:

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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

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