Hi Tim, If model #1.1 is a pseudobond model (e.g. missing segments or hydrogen bonds) you can show all those pseudobonds in a single color with color #1.1 halfbond false If you want one particular pseudobond to be a single color then select it by ctrl-clicking on it with the mouse and use color sel halfbond false If you want to only change the pseudobonds connecting atoms in chain B of atomic model #1 use color #1/B what pseudobonds halfbond false Unfortunately due to a bug that also changes the coloring of normal covalent bonds to be a single color. You can fix that by changing the covalent bonds back to halfbond coloring with color #1/B what bonds halfbond true I've fixed that bug in the August 22, 2026 ChimeraX daily build, so that second command to fix the covalent bonds will not be needed. ChimeraX color command documentation is here https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple Tom
On Aug 22, 2026, at 6:45 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I want to set halfbond false for a pseudobond in #1.1/B what is exact command? - Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/