Hello all, I am trying to perform a simple task using phenix.reflection_file_converter on the command line, but I am not getting the results I want and would be happy to receive advice as to how to do this properly. I am using Phenix 2.1-6048 on an Apple M3 Pro laptop. The input is a scaled and merged reflection file in MTZ format containing F, SIGF, IMEAN, and SIGIMEAN columns. I want to (i) transfer all four existing columns to the output file and (ii) generate R-free flags. When I try phenix.reflection_file_converter scaled_and_merged_data.mtz --label="F,SIGF,IMEAN,SIGIMEAN" --generate_r_free_flags --r_free_flags_fraction=0.05 --mtz=output.mtz I get the error: Unknown --label=F,SIGF,IMEAN,SIGIMEAN If I use multiple --label flags: phenix.reflection_file_converter scaled_and_merged_data.mtz --label="F,SIGF” --label="IMEAN,SIGIMEAN" --generate_r_free_flags --r_free_flags_fraction=0.05 --mtz=output.mtz the process executes successfully, but only the I columns from the second --label flag are present in the MTZ output. The first --label flag was not transferred to the output. I can create the desired output containing both F's and I's using the Phenix GUI, but I need to do this from the command line for scripting purposes. What is the proper command line syntax for transferring all existing columns to the output? Thanks, Matthew ____________________________ Matthew J. Whitley, Ph.D. [c] Scientist, RAS Structural Biology Group Cancer Research Technology Program (CRTP) Frederick National Laboratory for Cancer Research National Institutes of Health ATRF Room C1024 [email protected]mailto:[email protected]