Hi Yuri,
a possible way to show this simply involves these two steps:
1) make sure the model is as good as it can possibly be. This
seems trivial and obvious, but that's the tough one, and most
important too. At 1.18A it means: you included H atoms properly
(yes - properly!), you modeled all alternative conformations, you
modeled all solvent fully and partially occupied, you properly
parametrized the model, etc... etc... (very long list).
All in all, it means you reduced the noise low down enough so
you can see important signal.
2) after you fulfilled "1)", calculate various maps (residual,
OMIT, etc) and focus on diferences that you believe is the result
of catalysis.
I have breathtaking examples where the above 1)-2) steps really
work, which I think to publish one day (in CCN of course!).
I believe this strategy may work for you too.
Pavel
On 9/12/12 11:31 AM, Yuri wrote:
Hi everyone,
I am trying to show that a ligand underwent catalysis during a
soaking experiment.
One of the things I would like to show is the geometry of the
ligand, bond angles/lengths, dihedrals, etc...
One of my models has a hi-res of 1.18A and the ligand density is
really clear and complete.
What is the best way to refine the ligand unrestrained and then
generate measurements?
Also, the idea is to finally compare to ideal geometry. How should
I generate these values (any softwares in mind)?
ANy idea is welcome.
Thanks a lot