Hi Maia, 1) You can use phenix.refine for this: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1 output.prefix=maps_only Remarks: - you need to use strategy=none to tell phenix.refine to not refine atomic parameters (such as B-factors, coordinates, etc.); - you need to use "main.number_of_macro_cycles=1" (or its shortcut "main.number_of_mac=1"), so phenix.refine does bulk-solvent correction and anisotropic scaling, which is critical to get good maps. - of course, in twin-refinement, you also need to append a twin law to the above command, for example: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1 output.prefix=maps_only twin_law="k,-k,-l" 2) You can use new PHENIX GUI for this, just type: phenix.create_maps 3) Recent version of phenix.model_vs_data has "--map" keyword: phenix.model_vs_data model.pdb data.mtz --map="2mFo-DFc" Pavel.
I remember, there was a question how to generate maps without refinement. I finished the refinement, but I need a map (in explor format) to show the 2fo-fc density in the publication.