Hi James, This answer is for ChimeraX: If it is an enclosed surface (no openings, i.e. not a tunnel) you can use command "measure volume" <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#volume> For protein pockets/cavities in general see the new Find Cavities tool and "kvfinder" command (you need ChimeraX v1.9 release candidate or a newer daily build): <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/kvfinder.html> However, be aware that different adjustable parameters (and different pocket-finding methods, if you try comparing with other programs) will change the definitions of exactly where the molecular surface lies and where the "top" of a pocket is drawn, so it is best for only making comparisons among different pockets/tunnels calculated with the same set of parameters. 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 Nov 20, 2024, at 3:25 AM, Vitali James via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera support,
Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x.
best,
James