[Chimera-users] Coloring peptide bonds in Chimera

Tynan A. Becker tabecker at alaska.edu
Mon Jan 18 17:15:44 PST 2021

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,

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