Dear Sakia, The "measure sasa" command has a "probeRadius" option, see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> Example to measure sasa of model #2 with probe radius 0.8 Angstroms: measure sasa #2 probeRadius 0.8 However: This was mainly intended for use on organic compounds and biomolecules, not metal nanoclusters. So depending on the shape of your nanocluster, it may be difficult to get a meaningful result. Also, the radius of your metal atoms is just as (or even more) important than the probe radius, so you should check that and change it to whatever you think is the correct value before measuring surface area. ChimeraX will probably try to guess an ionic radius but if you have neutral metal atoms, it will probably not be correct. You can check the radius of an atom by selecting it (Ctrl-click) and then clicking the green magnifying glass icon on the top bar to show the Selection Inspector. You can also change it in there, but to change many atoms at the same time it may be more convenient to use the "size" command instead. See the help pages: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.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 22, 2023, at 8:44 PM, Sakiat　Hossain via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Sir/Madam, Greetings. I am a nanomaterial chemist, and I would like to measure solvent accessible surface area (sasa) of my metal nanocluster using its single crystal x-ray diffraction structure. Specifically, I want to calculate H+ accessible surface area. I would appreciate it if you kindly let me know how to change probeRadius for calculating sasa in ChimeraX. I look forward to your kind help. Best, Sakia Hossain Tokyo University of Science, Japan