If your starting model of the wild-type complex is good, you can probably get a decent estimate of the mutant structure with ISOLDE. Assuming your model is #1, first restrain everything to the existing geometry with: isolde restrain distances #1 displayThreshold 0.1 isolde restrain torsions #! Then introduce your mutations with swapaa (I recommend `swapaa mousemode` for this because it keeps the sidechain hydrogens). Start a simulation encompassing the interface region, and try to find the most sensible conformation for each mutant site. If you need to, you can selectively release restraints on the currently selected atoms with: isolde release distances sel isolde release torsions sel ... or, if you first do: isolde shorthand then for the rest of the session, you can replace the above with `rd` or `rt` respectively (or `ra` to release both distance and torsion restraints). Best, Tristan On Mon, Jul 24, 2023 at 6:14 PM Eric Pettersen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Begin forwarded message:
*From: *Krishnan Raman <RKrishnan@BIOCRYST.com> *Subject: **depicting contacts* *Date: *July 24, 2023 at 9:50:11 AM PDT *To: *"chimerax-users-owner@cgl.ucsf.edu" < chimerax-users-owner@cgl.ucsf.edu>
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
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