Hi Yoseph, The ChimeraX convexity measurement is used in the "measure convexity" command described here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#convexity The "cone angle" means the solid angle (steradians) spanned by the adjoining triangles, ie the area on a unit sphere enclosed in the pyramid made by the triangles with center at the vertex. So that value ranges from 0 to 4*pi and the convexity returns 2*pi minus (solid angle) so that will range from -2*pi to 2*pi with negative values meaning the cone is an indentation in the surface and positive values indicating a bulge in the surface and a 0 value meaning flat or a saddle shape. The C++ code that implements that calculation is on github and has a comment that clarified this // // Return convexity values for each vertex defined as 2*pi - (cone angle) // where the cone is formed by the triangles that share that vertex and // faces toward the surface interior (counter-clockwise righthand normal // points to exterior). Cone angle is steradians (surface area on unit sphere). // https://github.com/RBVI/ChimeraX/blob/5b3ddc2fdb186aec13579a295cc309584db6d2... https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/surface/_surface/c... Tom
On May 7, 2024, at 10:17 AM, Yoseph Loyd via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi ChimeraX Team,
My name is Yoseph, I'm a student. I saw that your measure convexity function 'vertex_convexity' is documented to report the vertex convexity from ' 2pi - half cone angle of the incident vertex and all triangles the incident vertex is a part of'. Is the half cone angle generated by averaging all half cone angles? Thank you for taking the time to read this and I hope your day goes well.
Best regards, Yoseph Loyd _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/