[phenixbb] ambiguous ligand density

Edward A. Berry BerryE at upstate.edu
Wed Mar 9 10:26:27 PST 2011

Could it be bonding a water molecule which is not modeled,
which in turn is binding the protein (water-mediated H-bond)?
You don't mention the resolution of the structure or whether or not
waters were modeled, or how unambiguous is the orientation of the ligand.

And what did the average kick and SA composit omit-map prior to
modeling in the ligand show that led you to be really lost?
Perhaps the ligand is not there at all?

If the density is really ambiguous it may not be possible to build the
ligand with certainty, but looking at the H-bonds in different
orientations as you are doing could be a basis for preferring one over another.


Pompeu,Yuri Alexey Andreiw wrote:
> Sorry, I meant judging by distances it is not experiencing interaction
> in the form of H-bonds.
> Which I think is concerning.
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