Well, it's beyond the scope of this helpdesk to consult on research projects in detail -- i.e. you'll have to use your own scientific judgment -- but here are some thoughts related to ChimeraX and what tools it provides. ChimeraX does not predict conformational/functional changes from a mutation. You can simply "mutate" amino acid sidechains with the swapaa command or Rotamers tool, but it does not predict or propagate any structural changes to the backbone or the rest of the structure. ChimeraX has interfaces to running several protein structure prediction programs (AlphaFold, ESMFold, Boltz, OpenFold) into which you can put sequence(s) and get out a 3D structure. However, whether they are suitable for predicting the effects of point mutations is not well established as far as I know, since they use evolutionary information from natural proteins in the form of a large sequence alignment. Also, the size of structure you can predict is somewhat limited. All of the above tools and commands are documented, see the User Guide. <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html> Regardless of how you get the mutated 3D structure, some analysis possibilities: a simple comparison of contacts, H-bonds, clashes, etc. gained or lost, or changes in relevant protein surface properties (coloring by electrostatic potential or molecular lipophilic potential). For all these kinds of analysis see the "Protein-Ligand Binding Sites" tutorial as well as the manual pages of all of the individual tools and commands in the User Guide (link above) <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> Which analyses are most relevant depend on what information and experimental data you have about these specific proteins. It's possible that the mutation actually makes them misfold and/or degrade quickly in the cell so you'd be wasting time analyzing some imaginary structure. There are certainly other tools/programs and maybe even web services (outside of ChimeraX) that are meant specifically to predict the effects of mutations, but I don't have a list. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Mar 6, 2026, at 6:03 AM, via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

I am working on a project regarding evolution and want to be able to make the necessary mutations on the proteins and then be able to visually see the impact the mutation has on the interaction of the proteins. Specifically, I want to be able to use this information to create a hypothesis as to why these proteins evolved based on the change in interaction. I have tried measuring the distance between the two proteins, but I was wondering what would be the best way to see the biological relevance and overall structural impact of the mutations?

Thanks! _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/