[phenixbb] how to extend R-free set

[Francis E Reyes]

Curious, will either of the utilities (iotbx.reflection_file_editor or  
iotbx.r_free_flags_completion_simple) follow --use-lattice-symmetry-in- 
r-free-flag-generation that phenix.reflection_file_converter offers?


Thanks

F

On May 19, 2010, at 10:20 AM, Tom Terwilliger wrote:

> Hi Robert,
> You can do this really easily in the PHENIX GUI with the reflection  
> file editor.  If you want to use a command-line tool you can also  
> use iotbx.r_free_flags_completion_simple.
> All the best,
> Tom T
>
> On May 19, 2010, at 10:18 AM, David Cobessi wrote:
>
>> Hi Robert,
>> Using CCP4... ;-)  (maybe Freerflag) you can do it....
>> David
>>
>> Robert Immormino wrote:
>>> Hi,
>>>
>>> Hopefully I'm just missing something obvious....
>>>
>>> I'm trying to copy the Rfree set from an old set of data, to a new
>>> mutant structure....and extend to higher resolution.
>>>
>>> I've tried:
>>>
>>> phenix.reflection_file_converter old.mtz --label="R-free-flags"
>>> new.sca --label="i_obs,sigma" --mtz new.mtz
>>>
>>> and several other combination, but I am still failing to get  
>>> phenix to
>>> read multiple data files and output the desired mtz.  I can get just
>>> the Rfree flags or the I and SigI, but not both.
>>>
>>> I also tried with phenix.refine
>>>
>>> phenix.refine --dry-run old.pdb old.mtz new.sca ligands.cif
>>> refinement.input.xray_data.labels="i_obs,sigma"
>>> refinement.input.xray_data.r_free_flags.label="R-free-flags"
>>>
>>> This seems closer, but I get the error:
>>>
>>> Sorry: R-free flags not compatible with F-obs array: missing flag  
>>> for
>>> 492 F-obs selected for refinement:
>>>
>>> Thanks,
>>> -bob
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>
>>
>> -- 
>> David Cobessi
>> Institut de Biologie Structurale
>> 41, Rue Jules Horowitz
>> 38027 Grenoble Cedex-1, France
>> Tel:33(0)438789613
>>   33(0)608164340
>> Fax:33(0)438785122
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel:  505-667-0072                 email: terwilliger at LANL.gov
> Fax: 505-665-3024                 SOLVE web site: http:// 
> solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org
> ISFI Integrated Center for Structure and Function Innovation web  
> site: http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ 
> cbss
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100519/286c3cce/attachment-0003.htm>