[Chimera-users] Calculating surface area of a single atom

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 1 09:42:31 PDT 2018

The surface calculation is not meant for single atoms.  Even if it did work on single atoms, the radius would not be appropriate because the H radius in Chimera program is only meant for H bonded to other atoms in the context of a molecule.

You have to research for yourself the radius you think is correct for what you want to do, and then just use simple geometry to calculate the area of a sphere with that radius, or for that radius + 1.4 if you are trying to get some (very approximate) solvent-accessible surface.

Google “area of sphere” to see the formula.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 1, 2018, at 7:57 AM, 김민재 <kjh950429 at gmail.com> wrote:
> Hey everyone!
> I've been trying to calculate the solvent excluded surface area of a single hydrogen atom, but Chimera keeps returning an error "miscalc code 5" message whenever I run the "surface probeRadius" command. 
> I would really appreciate anyone's help.

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