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

Pavel Afonine pafonine at lbl.gov
Sat Mar 12 20:47:16 PST 2011

  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..


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