Hi Nathan, If you generate an omit map with two_fofc_in_rebuild=True then all your maps should come from phenix.refine and be the 2FOFCWT PH2FOFCWT maps which are not density modified. It may be slightly confusing because the names of the files will remain the same, and you'll want to look through the log file to confirm that these are indeed the maps from phenix.refine. It will say something like: Saving 2fofc information in cycle_best_2.mtz NOTE: 2fofc map to be used for model-building. It will be copied to overall_best_refine_map_coeffs.mtz and will also be copied to overall_best_denmod_map_coeffs.mtz All the best, Tom T Hi, Is there is a way to calculate simple omit maps and sa-omit maps in phenix without using density modification? The density modification seems to be flattening the weaker regions of my map - when compared to omit maps from cns for instance. Thanks! Nathan _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb