Hi, Sorry, the cartoon is in single-residue segments that approximately represent the whole backbone (N,CA,C). So you either have to show the whole cartoon for that residue, which starts before the CA, or hide it, but then cartoon would not start until the second residue backbone (at the next N, approximately). Similarly you can't make half of it transparent either, since it is controlled only per residue. I couldn't think of a way to make the cartoon do what you want, but I had one idea using a different type of display: If you are not showing cartoon helix and strand representations but instead just a tube (e.g. what you get from command "preset licorice") instead of the cartoon you might try using "shape tube" and explicitly using only the atoms you want to define it. open 1gcn hide cartoon show atoms shape tube @ca radius 0.5 See "shape" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html> 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 Jan 27, 2024, at 2:14 PM, Hirbod Heidari via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi everyone,

I've been working on a protein display that I want to explicitly show the sidechain and backbone atoms of the N terminal residue. The problem is with the cartoon representation. For the N terminal, the cartoon rep goes beyond the CA atom and sticks out. Any tip on how I can change it? I thought of eliminating the pseudobond representation for the CA atom so that the cartoon representation doesn't happen between C and CA but it did not work for me.

Thanks!