[Chimera-users] Coloring peptide bonds in Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 19 08:43:45 PST 2021

Hi Tynan,
For a real bond (not chain trace):

(1) select the bond (Ctrl-click on it, shows green selection outline)
(2) open the Selection Inspector by clicking the green magnifying glass icon near the bottom right of the Chimera window, it will be set to Inspect: Bond
(3) in the Selection Inspector dialog, change halfbond mode to "off" and click the square next to "color" to open the Color Editor to change the color interactively.

Screenshot below.  If you are showing chain trace those sticks are pseudobonds, not bonds, and you can do the same steps as above, except that you have to change the Selection Inspector to Inspect: Pseudobond. 

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 18, 2021, at 5:15 PM, Tynan A. Becker <tabecker at alaska.edu> wrote:
> Good afternoon,
> I have been trying to figure out how to color just a single peptide bond between 2 residues in a protein.
> What I have figured out so far is to show chain trace under actions|atoms/bonds.  Then invert the selection (whole protein). This shows the bonds.
> I can select a residue and color the bond on both sides.  But I want to color the bond between 2 residues.  If I pick the bond by manual selection, the action|color|choice doesn't work.  The manual tantalizingly suggests using the "halfbond" setting or "bondcolor" for the command line.  The problem that I encounter is that I can't figure out how to tell the program which bond I want.  I've read the "atom specifications" page of the manual and tried every logical combination I can figure to tell the program which bond I want to color.  But each time, I get the "mangled atom specifier" error.
> I was told today that there is a way to do this, but I'm stuck. Any input is welcome.
> Thank you,
> Tynan
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