Re: [phenixbb] R free set in twinned dataset

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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