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