Sorry, ChimeraX does not have Surfnet or Intersurf tools. In ChimeraX, for finding pockets and tunnels in structures, see the Find Cavities tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/findcavities.html> <https://www.rbvi.ucsf.edu/chimerax/features.html#kvfinder> Another possibility is to use the MOLEonline web server and then use ChimeraX to display and color the results, as in this tutorial: <https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html> For interface analysis, see commands "interfaces" and/or "measure buriedArea" and/or "surface zone" <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedare...> <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#zone> For example, to show surface of chain /A within 5 Angstroms of atoms in chain /B in hemoglobin: open 4hhb surface hide surface surface zone #1.2 near /B distance 5 In the example above, "surface" creates the surface for the 4 chains of hemoglobin and you can see in the Models panel that the surface for /A is #1.2, surface for /B is #1.3, etc. It is necessary to create the surface and then hide it before using "surface zone" to show only a part of it. Regards, 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 Jul 22, 2025, at 6:40 AM, mlopez--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good afternoon, Does anyone know where are the Intersuf and the Surfnet options in ChimeraX?. Thanks a lot.