Hi All, Sorry if this is a trivial question. I'm refining my first structure at 2.1 A resolution. There is no density for the main chain carboxyl oxygen of a residue even at 0.5 sigma level in 2FoFc map. The FoFc map shows a negative density when I place the oxygen, satisfying the standard geometry condition. Could someone tell me what to do in this situation. Should I make the occupancy of the oxygen zero. Any comments would be gratefully appreciated.
Thanks very much. John Peter
