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/

Hi Tim, You may be having trouble bringing up the menu because it is control-double-click that brings it up. If that takes a little too much dexterity, you can just control-click to select the pseudobond and use the command "delete pseudobonds sel" (or "del ps sel" for short) to delete the pseudobond. Hiding the pseudobond ("hide sel") might be preferable in some situations. --Eric Eric Pettersen UCSF Computer Graphics Lab

On Aug 26, 2026, at 7:17 AM, Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Thanks Tom, this is very helpful. What is the command to delete a specific pseudobond for a missing segment? Sometimes I can click on it and the option pops up, but it is hard for me to reproduce it. - Tim Timothy A. Springer, Ph.D. Latham Family Professor, Harvard Medical School and Boston Children's Hospital Founder, Institute for Protein Innovation

On Sat, Aug 22, 2026 at 8:00 PM Tom Goddard <goddard@sonic.net> wrote:

...

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/

_______________________________________________ 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/