[phenixbb] R free set in twinned dataset

[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 <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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