Hi Nikhita, ChimeraX uses a standard analytical calculation of solvent accessible surface area. I don't know if it is the Lee and Richards method. I wrote the ChimeraX code for this and a description of it is here. https://www.cgl.ucsf.edu/chimera/data/sasa-nov2013/sasa.html It computes the exact areas of the spherical polygons that make up the solvent accessible surface. It shouldn't matter what the calculation method is if it is an exact (rather than approximate) method. But what will matter and will surely be a problem is that the area values depend on the atom radii, and everyone uses different atom radii. So your reference residue areas will be with whatever atom radii those authors decided to use and won't be the same as ChimeraX atom radii. ChimeraX atom radii are described here https://www.cgl.ucsf.edu/chimerax/docs/user/radii.html Tom
On Jun 15, 2025, at 9:44 PM, komatireddy.nikhita--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Sir/Madam,
I am Nikhita, an undergraduate student working on a research project and I am considering to use ChimeraX to calculate solvent accessibility surface area (SASA) for some residues of a protein. However, since I would like to calculate relative solvent accessibility surface area manually, I am using the reference maximum SASA values from Tien et. al. (2013) which mentions that using softwares that calculate SASA using the Lee & Richards method are preferable. As such, I would like to ask if ChimeraX uses the Lee & Richards method to calculate SASA as I could not find much about this on the ChimeraX website. 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/