[phenixbb] R free set in twinned dataset

Peter Zwart PHZwart at lbl.gov
Mon Oct 8 14:12:42 PDT 2007


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 <jzhu at cbr.med.harvard.edu>:
> 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 <jzhu at cbr.med.harvard.edu>:
> 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 <jzhu at cbr.med.harvard.edu>:
> 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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