[phenixbb] how to extend R-free set

[Tom Terwilliger]

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
>> _______________________________________________
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>>
>>
>
>
> -- 
> 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
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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