Hi Appu, You should be able to make a sa-omit map the same was as you make an omit map if you include the keyword composite_omit_type=sa_omit (see http://phenix-online.org/documentation/autobuild.htm#anch173): Make a SA-omit map around atoms in target.pdb phenix.autobuild data=data.mtz model=coords.pdb omit_box_pdb=target.pdb composite_omit_type=sa_omit Let me know if that doesn't do it! All the best, Tom T On Dec 7, 2012, at 3:41 AM, Appu kumar wrote: Dear Users, I am refining a enzyme structure with ligand. I want to make the simulated annealing omit map of ligand including with 4 Angestron radius around the ligand. I am seeking your valuable advice to help me out. I know how to make omit map but i have not come accross making simmulated annealing omit map. I would appreciate your help. Thank you Appu _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb