[phenixbb] most appropriate map for ligand fitting/interaction with FMN

[Yuri]

I am refinig a structure at 2.1 A. I have 2 questions:
a) Is the best way to identify a ligand refining the protein and water 
molecules and at the end looking at the 2mfo-dfc and mfo-dfc maps? Or 
looking at a SA composit omit map?
b) In almost every map i look at during refinement I see density that 
smears/joins my ligand (cyclopentenone type molecule) and flavin's 
isoalloxazine ring. Has anyone ever seen that? they seem to be 3.1 A 
apart?

Thanks


--
Yuri Pompeu