Hi Haley, It would be helpful to say what RSA is, but I'm guessing you mean relative surface area. ChimeraX does not calculate relative surface area (% exposed relative to some reference state). With "measure sasa" you can get solvent-accessible surface area and assign values per atom and per residue as an attribute named "area", which can be saved to a text file with "save" or reported in the Log with "info residues". See help pages for command details and options not mentioned here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> You can control whether it is considering a chain in isolation or the whole complex when calculating these values, by what you specify in the command. For example, this would consider the protein part of chain A in isolation and ignore where it is buried by other chains: measure sasa /A & protein ...whereas this would consider all the protein chains together, where parts of some chain may bury parts of some other chain: meaure sasa protein Then save or report in Log, e.g. info residues protein attribute area info residues protein attribute area saveFile myoutputfile.txt - or - save myoutputfile.defattr attrName r:area (the latter uses "r:" to mean residue, if omitted you will get areas per atom instead) However, what you get are simply the square angstroms of area, not "relative" (normalized) values. See previous discussion on this topic: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> 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 4, 2026, at 6:37 AM, Haley Breckenridge via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good morning,
Is there a way for ChimeraX to calculate RSA values on a per residue basis for an entire structure? I've found software online that can do it by chain, but my structure is made of multiple overlapping chains that would impact RSA values. I understand there is the Interface function in ChimeraX, but I cannot find a way for it to tell me RSA values for each residue in a structure.
Thanks! Haley Breckenridge