Thank you very much Elaine for clearing it up! It helped a lot, I appreciate it. Best Sayeeda ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, September 15, 2025 4:28 PM To: Kazi Sayeeda <SayeedaK@upstate.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] Guidance on SASA/RSA calculation in ChimeraX Dear Kazi, This is a misunderstanding of how "measure sasa" works. It will actually enclose the specified atoms in a surface and give you the area. Instead, you probably want the whole protein enclosed in a surface (not just a surface around Dear Kazi, This is a misunderstanding of how "measure sasa" works. It will actually enclose the specified atoms in a surface and give you the area. Instead, you probably want the whole protein enclosed in a surface (not just a surface around the single residue) and then you just want the area of the part contributed by that residue. If you measure sasa of the whole protein, the "setAttribute true" option will then also save an attribute named "area" per residue which is its SASA in the surface of the whole protein. This is explained in the help: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...> So instead of measure sasa #1:92 measure sasa #1:562 ...you'd probably want something like measure sasa protein setAttribute true info residue #1:92 attribute area info residue #1:562 attribute area However, there may be differences from the atom radii in ChimeraX and the atom radii used by Tien et al. The probe radius could also be different, but you can easily set it in ChimeraX with the "probeRadius" option of the "measure sasa" command (see help link above). For exact consistency with Tien et al. you would also need to know what atom VDW radii they used. Here are the ChimeraX defaults, but you can change them with the "size" command <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/radii.h...> <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/command...> It might be a pain to generate your own maxSASA, since you'd need to generate all the reference-state peptides -- I don't know what Tien used, but I know some people used extended gly-X-gly tripeptide where X is the residue type you are getting the maxSASA for. 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 Sep 15, 2025, at 10:13 AM, Kazi Sayeeda via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Support Team, I am currently using ChimeraX (v1.10.1) to study whether certain amino acid residues are surface-exposed or buried in my protein structures (WT and mutants from AlphaFold/NeuroSnap). To assess this, I measured solvent accessible surface area (SASA) with the following commands: measure sasa #1 measure sasa #1:92 measure sasa #1:562
This gives me the following SASA values (in Ų): • WT Ala92: 216.4 Ų • WT Gly562: 189.0 Ų When I compare these to published maximum ASA (MaxASA) values from Tien et al. 2013 (probe radius 1.4 Å): • Ala (max ASA) = 129 Ų • Gly (max ASA) = 104 Ų I get relative solvent accessibility (RSA) values greater than 1: • Ala92: 216.4 / 129 = 1.68 • Gly562: 189.0 / 104 = 1.82 Since RSA should not exceed 1, I believe I am mismatching ChimeraX’s calculation settings with the MaxASA reference set. So my questions are: • What radii model and probe radius does measure sasa in ChimeraX use by default? • Is there a way in ChimeraX to directly assign per-residue SASA attributes and normalize them internally (so RSA values remain ≤1)? • If ChimeraX defaults differ from published MaxASA tables, would you recommend reporting only SASA values, or generating my own MaxASA reference values with ChimeraX for consistency? I would be very grateful for any guidance or documentation pointers so I can report values in a way that is consistent and interpretable. Best,
Kazi Sayeeda PhD Candidate Dept. of Cell and Developmental Biology (Krendel Lab) SUNY Upstate Medical University Syracuse, NY 13210
sayeedak@upstate.edu