Sorry for a very basic question about generating an omit map.

I am trying to generate a SA-omit map for only my ligand but not the protein core of my complex.  I presume I can use phenix.composite_omit_map GUI and specify my ligand chain in Atom Selection? 

All other parameters being the same, I notice that when I did not select any atom the whole structure was divided to 30-40 regions but when I selected my ligand chain it now divides into 89 regions. Is there a reason why and is there any advantage to manually adjust the number of omit regions?

Many thanks and regards