Hi Andy, If you use the "measure sasa" command with "setAttribute true" (default) it will create an attributes of atoms and residues named "area." See the help page for complete information on this command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> Be careful to exclude waters, etc. from the atom specification, or delete them before doing the calculation, since they won't automatically be ignored. There is an example command in the help that shows calculating the SASA based on protein atoms only. Then you would need to decide what minimum value qualifies a residue as being exposed, since zero is probably too low (or try a few different values and see what you think is reasonable). The "area" attribute created by "measure sasa" would show up in the Render by Attribute dialog. You should use ChimeraX 1.6 or newer for the latest features in the Render by Attribute tool. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 14, 2023, at 4:15 PM, Andy Nguy via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I was wondering if there is a AreaSAS function for ChimeraX. To my knowledge, there was such a function in Chimera under "Render by Attribute". If not, is there a way to identify all solvent-accessible residues for a protein of interest? Thanks! -- Andy.