[phenixbb] refinement of a ligand with alternate conformations in one region but not the other.

[Pascal Egea]

Dear All,
I am refinining a protein-NAD complex structure at ~1.9A resolution.
I have included a main conformation for my NAD ligand but while I see
clearly the position for the nicotinamide- first ribose part, my density
bifurcates when it comes to the second ribose-adenine. It seems that I have
two (at least) conformations for this part of the ligand molecule.

Can I refine these two alternate conformations in Phenix knowing that a part
of the ligand will be common (have an occupancy of one) while the two other
ones will be separate?

Do I need to enter two ligand molecules or do I have to do more elaborate
things?

Last question is it possible that for the variable regions I may end up with
a sum of occupancies that is not 1 while for the fixed region it might end
up being one?

That's three questions for the wizards.

Thanks in advance.

Pascal Egea
UCSF
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