HI Nikhita, One possibility is to try to change to the same radii as that paper used before calculating SASA in ChimeraX. It depends whether they give the full information of what radii they used, and how much work you are willing to do (how many ChimeraX "size" commands) to make the ChimeraX radii the same. ChimeraX "size" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> The other possibility is also a lot of work. You'd have to create all the reference states (something like extended Gly-X-Gly tripeptides is what some people have used, where X is each of the 20 standard types of residue) and measure the SASA of the "X" residue in each one in ChimeraX as a representative of the exposed area of that residue type. Then you would have your own set of reference values using the ChimeraX radii. 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 Jun 16, 2025, at 9:12 PM, komatireddy.nikhita--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Tom,
I would also like to check if there is a way to directly calculate relative solvent accessibility surface area via ChimeraX instead of manually comparing SASA with reference values from a separate paper and perhaps this would also make it a more accurate method of obtaining relative SASA?
Thank you!
Warm regards, Nikhita _______________________________________________ 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/