Hi 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?
These are good to look at. This is why phenix.refine outputs them. Ligand-omit kick map may be a quick way of getting less model biased residual omit map for your ligand.
Or looking at a SA composit omit map?
This may may be useful if you want to prove something or in doubt.
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?
I'm not quite sure what you mean - it's hard to discuss a map without looking at it.. Pavel.