[phenixbb] how to extend R-free set

Pavel Afonine PAfonine at lbl.gov
Wed May 19 09:13:05 PDT 2010

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.


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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