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 +++++++++++++++++++++++++++++++

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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 +++++++++++++++++++++++++++++++

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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.

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 +++++++++++++++++++++++++++++++

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