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Hi, Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual. Thanks. 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 +++++++++++++++++++++++++++++++
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Yes.
phenix.refine will take into acocunt all possible twin operators for
the given crystal symmeytry.
Even in the absence of a supplied twin operator, the free set will be
chosen in a sensible manner.
HTH
Peter
2007/10/8, Jianghai Zhu
Hi,
Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual.
Thanks.
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 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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Thanks. How do I generate the R-free flag without any model refinement? I just want to output a new mtz file with the new R-free flags. 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 Oct 8, 2007, at 4:04 PM, Peter Zwart wrote:
Yes.
phenix.refine will take into acocunt all possible twin operators for the given crystal symmeytry. Even in the absence of a supplied twin operator, the free set will be chosen in a sensible manner.
HTH
Peter
2007/10/8, Jianghai Zhu
: Hi,
Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual.
Thanks.
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 +++++++++++++++++++++++++++++++
_______________________________________________ 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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use
phenix.reflection_file_converter input.mtz --mtz=output.mtz
--generate-r-free-flags \
--use-lattice-symmetry-in-r-free-flag-generation
--r-free-flags-fraction=0.1 \ --r-free-flags-max-free=2000
This should do the trick. If not, it will tell you what else to
specify to get it running
HTH
Peter
2007/10/8, Jianghai Zhu
Thanks. How do I generate the R-free flag without any model refinement? I just want to output a new mtz file with the new R-free flags.
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 Oct 8, 2007, at 4:04 PM, Peter Zwart wrote:
Yes.
phenix.refine will take into acocunt all possible twin operators for the given crystal symmeytry. Even in the absence of a supplied twin operator, the free set will be chosen in a sensible manner.
HTH
Peter
2007/10/8, Jianghai Zhu
: Hi, Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual.
Thanks.
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 +++++++++++++++++++++++++++++++
_______________________________________________ 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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Thanks. It works. If there is multiple twinning possibilities, should I give the exact twinning operator? or the program already considers all of them. Any suggestions to remove the old R-free memories? I normally use a simulated annealing at 5000 K. Don't know if there is any faster way to do it. 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 Oct 8, 2007, at 4:47 PM, Peter Zwart wrote:
use
phenix.reflection_file_converter input.mtz --mtz=output.mtz --generate-r-free-flags \ --use-lattice-symmetry-in-r-free-flag-generation --r-free-flags-fraction=0.1 \ --r-free-flags-max-free=2000
This should do the trick. If not, it will tell you what else to specify to get it running
HTH
Peter
2007/10/8, Jianghai Zhu
: Thanks. How do I generate the R-free flag without any model refinement? I just want to output a new mtz file with the new R-free flags.
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 Oct 8, 2007, at 4:04 PM, Peter Zwart wrote:
Yes.
phenix.refine will take into acocunt all possible twin operators for the given crystal symmeytry. Even in the absence of a supplied twin operator, the free set will be chosen in a sensible manner.
HTH
Peter
2007/10/8, Jianghai Zhu
: Hi, Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual.
Thanks.
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 +++++++++++++++++++++++++++++++
_______________________________________________ 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
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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Any suggestions to remove the old R-free memories? I normally use a simulated annealing at 5000 K. Don't know if there is any faster way to do it.
I saw cases where even simulated annealing didn't help; but this is relatively rare. You can do shake coordinates and B-factors and do refinement as many macro-cycles as necessary (eg., until the gap Rfree-Rwork does not grow anymore): phenix.refine model.pdb data.mtz modify_start_model.sites.shake=1.0 modify_start_model.adp.randomize=true Instead of modify_start_model.adp.randomize=true you can use modify_start_model.adp.set_b_iso=25.0 The values in modify_start_model.sites.shake=1.0 is something to play with, but something like 1.0 ... 1.5 is ok in most of cases.
![](https://secure.gravatar.com/avatar/52479a1c0ae25633ed06f5fea2d1d56a.jpg?s=120&d=mm&r=g)
I saw cases where even simulated annealing didn't help; but this is relatively rare. You can do shake coordinates and B-factors and do refinement as many macro-cycles as necessary (eg., until the gap Rfree-Rwork does not grow anymore):
phenix.refine model.pdb data.mtz modify_start_model.sites.shake=1.0 modify_start_model.adp.randomize=true
Instead of modify_start_model.adp.randomize=true you can use modify_start_model.adp.set_b_iso=25.0
The values in modify_start_model.sites.shake=1.0 is something to play with, but something like 1.0 ... 1.5 is ok in most of cases.
Is this coordiantes and B-factors shaking as effective as SA? I believe it should be much faster.
![](https://secure.gravatar.com/avatar/7984547b53fca6ae837ba286f9c92e29.jpg?s=120&d=mm&r=g)
The coordinates and B-factors shaking itself take fractions of a second. The question is how many refinement macro-cycles you will need to perform after that to make sure the memory is removed and proper R/Rfree values are recovered back (5 or 10 or 50 or ...?). As for the second part of your question -- I don't know and I don't think there is a definitive answer to this. I never did any comparisons. Pavel. Jianghai Zhu wrote:
I saw cases where even simulated annealing didn't help; but this is relatively rare. You can do shake coordinates and B-factors and do refinement as many macro-cycles as necessary (eg., until the gap Rfree-Rwork does not grow anymore):
phenix.refine model.pdb data.mtz modify_start_model.sites.shake=1.0 modify_start_model.adp.randomize=true
Instead of modify_start_model.adp.randomize=true you can use modify_start_model.adp.set_b_iso=25.0
The values in modify_start_model.sites.shake=1.0 is something to play with, but something like 1.0 ... 1.5 is ok in most of cases.
Is this coordiantes and B-factors shaking as effective as SA? I believe it should be much faster. _______________________________________________ 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)
it takes all into account, so you should not be in trouble, even when
you have processed your data in P1 and it actually is P321
regarding the momory of the R free set, I think what youpropose is okai.
Remove all waters, set all B values to the wilson B and do some SA.
There might be an option in phenix.refine as far as I recollect.
Cheers
Peter
P
2007/10/8, Jianghai Zhu
Thanks. It works. If there is multiple twinning possibilities, should I give the exact twinning operator? or the program already considers all of them. Any suggestions to remove the old R-free memories? I normally use a simulated annealing at 5000 K. Don't know if there is any faster way to do it.
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 Oct 8, 2007, at 4:47 PM, Peter Zwart wrote:
use
phenix.reflection_file_converter input.mtz --mtz=output.mtz --generate-r-free-flags \ --use-lattice-symmetry-in-r-free-flag-generation --r-free-flags-fraction=0.1 \ --r-free-flags-max-free=2000
This should do the trick. If not, it will tell you what else to specify to get it running
HTH
Peter
2007/10/8, Jianghai Zhu
: Thanks. How do I generate the R-free flag without any model refinement? I just want to output a new mtz file with the new R-free flags. 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 Oct 8, 2007, at 4:04 PM, Peter Zwart wrote:
Yes.
phenix.refine will take into acocunt all possible twin operators for the given crystal symmeytry. Even in the absence of a supplied twin operator, the free set will be chosen in a sensible manner.
HTH
Peter
2007/10/8, Jianghai Zhu
: Hi, Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual.
Thanks.
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 +++++++++++++++++++++++++++++++
_______________________________________________ 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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participants (3)
-
Jianghai Zhu
-
Pavel Afonine
-
Peter Zwart