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 Å²):

WT Ala92: 216.4 Å²
WT Gly562: 189.0 Å²

When I compare these to published maximum ASA (MaxASA) values from Tien et al. 2013 (probe radius 1.4 Å):

Ala (max ASA) = 129 Å²
Gly (max ASA) = 104 Å²

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