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

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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