Hi Mengbin, If you set your ligand occupancies to 0 or delete their coordinates, then you don't actually need to make an "omit" map because you've already omitted your ligand. So you can just run simulated annealing on that model, and your map is a SA-omit map. I can imagine that it may be difficult to require your ions to stay where you want them during the SA process. Unless they are right next to your ligand, normally I would not expect this to affect very much however. If after this process your protein density is very strong and there is no density for the ligand, then it would normally be a good idea to back up to the point where you put the ligand in to the model. You might have a close look at the map created just before you ever had the ligand there and ask whether the density is strong. If yes, then you could try to figure out the difference between that map and the one you just made. If no, then perhaps the ligand is not really present. I hope that helps! All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Mengbin Chen [[email protected]] Sent: Tuesday, December 11, 2012 2:42 PM To: [email protected] Subject: [phenixbb] SA Fo-Fc omit map 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