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