Hi Tobias, No screenshot attached, but no worries, it's clear what you mean! Those aren't artifacts, but tethers intentionally showing the correspondence of CA atoms with the ribbon where their paths diverge. However, yes you can hide them, just make the tethers 100% transparent, example command: cartoon tether opacity 0 You could also control shape, color, etc. if you ever want them shown, see "cartoon tether" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> The other way is to open the structure twice and use one copy for cartoon display and the other for atom display, but that's unnecessarily complex. 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 May 4, 2026, at 8:35 AM, Eulberg, Tobias via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX Development Team, I am working on visualizing the oxyanion hole in an alpha/beta hydrolase structure and have encountered a display issue that I hope you can help me resolve. What I'm trying to achieve: I would like to display the backbone atoms (N, CA, C, O, and amide H) of specific residues (residues 36 and 103) as sticks to highlight the oxyanion hole NH groups, while maintaining the cartoon representation for the entire protein including these residues. The problem: When I display both the cartoon and the backbone atoms as sticks for the same residues, ChimeraX creates conical/tapered transitions connecting the cartoon ribbon to the displayed atoms. These conical shapes obscure the backbone atoms I'm trying to highlight, particularly the amide NH groups that form the oxyanion hole. My question: Is there a way to display backbone atoms as sticks for specific residues while maintaining the cartoon representation for those same residues, without the conical transition artifacts? Alternatively, is there a recommended workflow for highlighting specific backbone atoms (particularly amide NH groups) in the context of a cartoon representation without visual interference? I've attached a screenshot showing the conical transitions that appear when both representations are active. Thank you for your time, any guidance would be greatly appreciated. Best regards, Tobias Eulberg