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<div class="moz-cite-prefix">Hi Yuri,<br>
<br>
a possible way to show this simply involves these two steps:<br>
<br>
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). <br>
<br>
<b>All in all, it means you reduced the noise low down enough so
you can see important signal.</b><br>
<br>
2) after you fulfilled "1)", calculate various maps (residual,
OMIT, etc) and focus on diferences that you believe is the result
of catalysis.<br>
<br>
I have breathtaking examples where the above 1)-2) steps really
work, which I think to publish one day (in CCN of course!). <br>
I believe this strategy may work for you too.<br>
<br>
Pavel<br>
<br>
<br>
On 9/12/12 11:31 AM, Yuri wrote:<br>
</div>
<blockquote cite="mid:c0578cdf72436e64f86a1f5591bdf175@ufl.edu"
type="cite">Hi everyone,
<br>
I am trying to show that a ligand underwent catalysis during a
soaking experiment.
<br>
One of the things I would like to show is the geometry of the
ligand, bond angles/lengths, dihedrals, etc...
<br>
One of my models has a hi-res of 1.18A and the ligand density is
really clear and complete.
<br>
What is the best way to refine the ligand unrestrained and then
generate measurements?
<br>
Also, the idea is to finally compare to ideal geometry. How should
I generate these values (any softwares in mind)?
<br>
ANy idea is welcome.
<br>
Thanks a lot
<br>
<br>
</blockquote>
<br>
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