[phenixbb] how to extend R-free set

[Pavel Afonine]

Hi Bob,

you can use "Reflection file editor" for this. It is available from 
PHENIX GUI. I'm not sure if the corresponding command line option 
exists, Nat knows this better.

Pavel.


On 5/19/10 9:09 AM, 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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