Christian

As Tom pointed out, you may need to use the nightly for phenix.combine_focused_maps.

ReadySet! does not currently work on mmCIF files so ignore any output from there.

"apply_cif_modification" is for changes to entities as when a polymer is formed so that is not your answer to restraints.

thank you for the quick reply. I got phenix.pdb_interpretation to run after also supplying the options "disable_uc_volume_vs_n_atoms_check=True" and "proceed_with_excessive_length_bonds=True". It would then later hang on a "Symmetry disulfide" step but at least I got the names of the missing residues. In case it is relevant, they are 4OC, G7M, MA6, UR3, IAS, 1MG, 2MA, 3TD, 6MZ and OMU. phenix.elbow with --final_geometry=... then produced the required cif files.

Great. Supply these to real_space_refine and you should be golden.