Hi Jill, Here are a couple of possibilities: (1) use the ChimeraX "shape" command to make a triangle surface and then measure its area. For example, something like the following commands (note colons before residue numbers, not commas as you tried with measure) if the new surface model were #3: shape triangle atoms #2/b:44@o:97@ca:57@hz3 measure area #3 See: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html#triangle> (2) Old-school geometry. It's a little longer but I was curious and looked it up, so I figured I might as well outline it here... You can calculate the area of a triangle from the lengths of its sides (the atom-atom distances) using Heron's formula: <https://en.wikipedia.org/wiki/Heron%27s_formula> Given the side lengths, here is a web server that does it for you: <https://www.omnicalculator.com/math/triangle-area> For example, ChimeraX commands to measure distance: distance #2/b:44@o:97@ca distance #2/b:44@o:57@hz3 distance #2/b:97@ca:57@hz3 ...and if that gives the triangle you want, enter those resulting values into the web server. Of course the units will be wrong there, just ignore them and do everything in angstroms instead... assuming that's what you wanted. 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 Jun 4, 2025, at 11:47 AM, jillian.baker--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX community,
I am trying to use the 'measure area' command to measure the area using three atoms (essentially trying to calculate the area of a triangle). I have come up with the script of "measure area #2/b:44@o,97@ca,57@hz3" with 2 being model ID, b being the chain, and then the numbers being residues and the atoms are followed by the "@" symbol. I don't quite get an error here, but I get back "No surfaces specified." I can't seem to figure out away to specify a surface or use a different command to calculate the between these three points. Any help with this would be greatly appreciated.
Thanks, Jill