Dear Phenix Users, I have been playing around with Phenix AutoBuild GUI to generate a fo-fc sa omit map of the ligand in a protein structure, and I have the input files as follows: output.mtz (data type:experimental data) ligand.pdb (data type: omit box atoms & ligands) ligand.cif (data type: restraints of the ligand) protein.pdb (data type: starting model) omit map type: simulated annealing omit region: omit around PDB fie I have set the occupancies of all ligand atoms zero and deleted the ligand coordinates in my starting model. After the run finished and I checked the refined coordinates and map.mtz in COOT, I found that there was no electron density around the ligand while the protein model was in electron density, which was exactly opposite of what I wanted before. Furthermore, I have 3 Mg2+ ions in protein.pdb file, all of which moved away from where they were after the refinement run, which was not wanted either. Could anyone tell me how to do the sa omit map of ligand correctly? Thanks in advance! Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania