Hi Erika, The pbonds are inherently atom-atom -- there's no option to "collapse" into residue-residue because you would still need to decide which specific atom-atom pbond you want to retain between any given pair of residues. However, you can certainly select and hide them. E.g. Ctrl-click to select the pbond, command "hide sel" ... or you can Ctrl-click to select one, Shift-Ctrl-click to select another without deselecting the first, Shift-Ctrl-click another, etc. to have several selected at once, and then collectively hide them, command "hide sel" <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html> <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> Generally the pbonds are only shown when the pair of atoms is shown, so hiding one of the atoms is another way to also hide the pbond. Of course, if you want to keep showing the atoms, just use the other method above. 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 Apr 28, 2026, at 8:01 AM, Weiskopf, Erika Nicole via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

I want to visualize atom-atom pbonds (generated through the contacts feature) as single residue-residue contacts. Is there a way to do this and/or a way to delete single pbonds I have selected to manually clean up the image?

Thanks, Erika