[phenixbb] Ligand geometry, Ideal vs. Observed
pafonine at lbl.gov
Wed Sep 12 12:26:33 PDT 2012
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.
On 9/12/12 11:31 AM, Yuri wrote:
> Hi everyone,
> I am trying to show that a ligand underwent catalysis during a soaking
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb