[phenixbb] omit map

Hi everybody, I would like to calculate the omit map around the ligand. I followed the documentation http://www.phenix-online.org/documentation/autobuild.htm#anch159 But the 2Fo density around the ligand is very poor. Any help is appreciated. Thanks Mary 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 Coefficients for the output omit map will be in the file resolve_composite_map.mtz in the subdirectory OMIT/ . An additional map coefficients file omit_region.mtz will show you the region that has been omitted. (Note: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz).