Hi Junjie, I changed the subject line to something descriptive so it will be easier to find in the archive. (1) That is a cartoon "tether" which looks different because it is not a bond. The sticks show the actual atom/bond positions, but where the ribbon path is smoothed, it may not pass through the exact CA position, thus the tether is drawn to show that it is really the ribbon for the same residue even though there may be a spatial gap between the ribbon and the CA atoms. By default the beta-strand ribbons are smoothed -- if not smoothed, they look very wavy. Tethers are explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> If you want to show atoms + ribbons but don't want to see any tethers, your choices are: (A) make tether completely transparent (e.g. command: cartoon tether opacity 0 ) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#tether> ...or if you are OK with seeing the tether but you want it a cylinder shape even though it's not a real bond, you can also do that with the "cartoon tether" command, see link above... (B) don't smooth the ribbon at beta-carbons (e.g. command: cartoon smooth 0 ) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> (C) show CA atom as ball or sphere which may be big enough to eliminate the spatial gap for some residues, but probably not all (e.g. command: style @ca ball ) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/style.html> (2) you could try doing it as a selection outline, e.g. only select that part. You can change selection outline color etc. with the "graphics selection" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> 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 Mar 1, 2025, at 8:55 PM, junjie han via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I hope you are doing well. May I ask two questions?

First one: Why does the connection part between the side chain and backbone, which is circled in a dashed line in ChimeraX, look so abnormal? How can I make it display normally?<image.png> Second one: Is it possible to show the border only for a specific region of protein without hiding other regions?

Thanks, Junjie