Hi Elaine Thanks for your reply. I managed to do it a different way. First change the bond color by selecting the atoms and then changing its color (which obviously changes the color of the atom too), then changing the color of the atom again to its original color. Best Faisal On Sun, Jul 6, 2025 at 3:55 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Faisal, You didn't say how you changed the color, so I don't know what was wrong.

If you really mean a bond (not a pseudobond), by default it only shows the colors of the atoms on both ends, instead of its own color.

Here is one way to change the bond color:

Select the bond (Ctrl-click) and then open the selection inspector (menu: Actions... Inspect, or click the green magnifying glass icon in the Home tab of the toolbar across the top). See <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html#bonds>

Then in the Selection Inspector, Inspect: Bonds. By default the "Halfbond mode" is turned on, which means to show only the colors of the atoms on the ends. So you can either change the colors of the two atoms on the ends of the bond (with Halfbond mode turned on), or you can turn off Halfbond mode, and then change the color of the bond. One way is to click the color square in the Selection Inspector to change the color interactively in your system color editor.

If it is a pseudobond and not a bond, you can use a similar process of selecting and then using the Selection Inspector. Some (but not all) kinds of pseudobonds already have Halfbond mode turned off by default. Also you may want to consider whether you want to change color for the whole "Pseudobond model" or just the individual "Pseudobond" -- see Selection Inspector help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html#pb-models>

Explanation of what is a pseudobond: <https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>

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

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On Jul 4, 2025, at 1:11 PM, khaja faisal tarique via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Hi

I am trying to color different bonds with different colors in ChimeraX, but when I select one bond and change its color so it gets applied to all bonds. Is there any trick to do that ? What I am doing is the Cltr+Bond to select a bond then changing color to that selected bond. But I do not why the change is applied to all other bonds.

Any help would be appreciated

Faisal

-- Faisal Tarique Khaja Research Associate Indian Institute of Science Bangalore, India