![](https://secure.gravatar.com/avatar/c59c83b372c7116eff6b73580ab053ed.jpg?s=120&d=mm&r=g)
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
![](https://secure.gravatar.com/avatar/52479a1c0ae25633ed06f5fea2d1d56a.jpg?s=120&d=mm&r=g)
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
![](https://secure.gravatar.com/avatar/52479a1c0ae25633ed06f5fea2d1d56a.jpg?s=120&d=mm&r=g)
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
![](https://secure.gravatar.com/avatar/ea71c539cb4346ef7ccd8150c668f6ce.jpg?s=120&d=mm&r=g)
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
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
![](https://secure.gravatar.com/avatar/52479a1c0ae25633ed06f5fea2d1d56a.jpg?s=120&d=mm&r=g)
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
![](https://secure.gravatar.com/avatar/ea71c539cb4346ef7ccd8150c668f6ce.jpg?s=120&d=mm&r=g)
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
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
participants (3)
-
Jianghai Zhu
-
Petrus H Zwart
-
Ralf W. Grosse-Kunstleve