Hi Zheng, Sorry, according to my tests, only these surfaces can be shown as solid at the clipping plane: (1) molecular surfaces (2) volume isosurfaces (e.g. for density maps) For the above, it can be controlled with "surface cap true" (or false to turn it off): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#cap> I thought it might be possible with the straight cylinders (e.g. shown with "define axis perHelix true" or "shape cylinder") since those are surface models, but I see that they are shown as hollow even if I used "surface cap true" -- tested in the current daily build. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 27, 2022, at 1:49 PM, Zheng Ruan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX users, I'm curious to know if there is a way to have the helix tube filled when after using the clip command? I know that the clip plane of surface representation can achieve this as found in this example (https://www.rbvi.ucsf.edu/chimerax/feature_highlights/pmc.png). However, I'm not able to make it when I display my structure in cartoon cylinder representation. I attached an example image that I made. Thank you for your input. Best, Zheng