[phenixbb] Ligand geometry, Ideal vs. Observed

Pavel Afonine pafonine at lbl.gov
Wed Sep 12 12:26:33 PDT 2012

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.


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

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