Sorry, there is no solution for this issue other than avoiding clipping the cylinders. No capping is provided for most graphical objects such as cartoon tube helices, stick bonds, and atomic representations. Although commands "shape cylinder" and "define axis" do create surface models with a cylindrical shape, they will also look hollow at most clipping plane orientations. If you do not clip these surface-model cylinders, they should look solid. However, if you have clipping planes intersecting them, they will look hollow at most clipping plane orientations. There is a very long explanation of why this is so, but the shortest I can come up with is that each surface cylinder is constructed as 3 separate surfaces, an open cylinder and the 2 circular end pieces, and they are not exactly joined up. So the clipping/capping code simply sees them as 3 already open surfaces and there is no capping at most angles. The possible solutions were determined to cause too many other problems like slower calculation of the cylinders and stuttering as they are rotated, with loss of interactivity, so developers do not plan to change this behavior. I hope this clarifies the situation, 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 Oct 14, 2024, at 11:14 PM, youngxiaolin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Sir/Madam, I am currently working on a cross-sectional visualization of a transmembrane helix bundle shown as cylindrical cartoon. I notice that, unlike in surface visualizations, my helices are not capped, leaving the ends exposed. Are there specific parameters or settings within ChimeraX that I should adjust to customize the appearance of the helix caps? Thank you in advance for your assistance. I am looking forward to your expert advice.

Best regards, Xiaolin Yang National clinical research center for Infectious diseases