Re: [phenixbb] ls_wunit_k1

All right. The target for my TLS is also LS. Is that intentional too? 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 25, 2007, at 10:55 PM, Petrus H Zwart wrote:

Yes.

It is more robust and used in the so called MZ protocol. It has a large radius of convergence.

Peter

----- Original Message ----- From: Jianghai Zhu Date: Sunday, March 25, 2007 6:25 pm Subject: Re: [phenixbb] ls_wunit_k1 To: PHENIX user mailing list

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The default target for rigid body is LS from "phenix.refine --show-

defaults=all". Is this intentional?

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 25, 2007, at 10:14 PM, Jianghai Zhu wrote:

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I checked my log file and didn't find "automatic adjustment". My main target is mlhl. However, the target function for rigid body is ls_wunit_k1. I didn't choose that. Is LS the default for rigid body?

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 25, 2007, at 10:00 PM, Ralf W. Grosse-Kunstleve wrote:

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You are right. Somehow, the default target function in refinement.bulk_solvent_and_scale is LS, not ML.

The default (phenix.refine --show-defaults=all) is actually ml. However, if the main target is set to ls the bulk_solvent_and_scale target is automatically reset to ls, too. There should be corresponding messages in the log file ("automatic adjustment"). Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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