[chimerax-users] Re: depicting contacts

Hi Krish, It is rarely possible to show some kind of obvious visual/structural correlate to energy improvements of a kcal or two from a simplistic approach to virtual mutation such as the sidechain swaps that ChimeraX does. One might need to do a full-scale new prediction of the mutant structure in some other program, or even do a long dynamics simulation (or free energy perturbation simulation with gradual mutation) to gain insights into the contributions to the change in affinity. It might be something quite subtle like changing the conformational entropy of the unbound state. Just my two cents' Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 24, 2023, at 10:12 AM, Eric Pettersen via ChimeraX-users wrote:

From: Krishnan Raman Subject: depicting contacts Date: July 24, 2023 at 9:50:11 AM PDT

Hi all, Any ideas to depict a dramatic improvement(200 nm to femtomolar) in binding affinities before and after mutations(about seven) in chimerax? II have tried contacts , swapaa etc. nothing seems dramatic enough for visuals Thanks