Greetings, I would be very grateful if someone can help me to explain in I can get F0-Fc omit maps of a particular ligands using Phenix. I am trying to generate an omit map for the ligands in my protein model using the composite omit map GUI feature of phenix version 1.10.1-2155. I selected my ligands by using atom selection feature under the map options(and in the omit map method I put refine). What map type I should give in the map types input to get the F0-Fc maps. Currently I may getting a map that look like my 2F0-Fc map that I got after my refinement. Also, I have no waters in my model. Can we define areas (boxes) around the ligand to generate omit map of that particular region to get output maps with densities like Fo-Fc maps. So many thanks in advance. Regards Manoj