Re: [phenixbb] ls_wunit_k1

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Re: [phenixbb] ls_wunit_k1

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ls_wunit_k1

Ralf W. Grosse-Kunstleve

25 Mar 2007 25 Mar '07

11 p.m.

...

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

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Jianghai Zhu

25 Mar 25 Mar

11:14 p.m.

New subject: ls_wunit_k1

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:

...

...
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

Jianghai Zhu

11:25 p.m.

New subject: ls_wunit_k1

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:

...

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:

...
...
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

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

Petrus H Zwart

11:55 p.m.

New subject: ls_wunit_k1

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

...

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:

...
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:

...
...
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

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

Jianghai Zhu

26 Mar 26 Mar

12:14 a.m.

New subject: 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

...
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:

...
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:

...
...
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

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

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

Petrus H Zwart

12:29 a.m.

New subject: ls_wunit_k1

I have seen that as well, not sure why that is. I guess it has to do with stability issues. Not sure if you can enforce the use of an ML target there. Peter ----- Original Message ----- From: Jianghai Zhu Date: Sunday, March 25, 2007 7:14 pm Subject: Re: [phenixbb] ls_wunit_k1 To: PHENIX user mailing list

...

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

...
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:

...
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:

...
...
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

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

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

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Jianghai Zhu
Petrus H Zwart
Ralf W. Grosse-Kunstleve