[Chimera-users] labeling residues

Daniel Gurnon danielgurnon at depauw.edu
Sun May 15 10:56:44 PDT 2011

Hi all,
A student of mine wants to make a wire sculpture of a protein, and I'm
thinking of ways Chimera could make the task easier. Ideally, I would create
a script that would display any protein in wire-form, with residue positions
clearly and unobtrusively labeled.

I'd like to use the command line to display a backbone as a licorice ribbon
with residue numbers and 1-letter codes at the alpha carbon of each residue.
so starting out, I would use:
ribscale licorice; ribbackbone; rlabel @ca;

But instead of "ALA 24.B", I want "A 24". Though I can get what I want using
the Actions menu, I can't find a way to create custom rlabels via the
command line. Is there a way to do this?

If possible, I would also like to position each label near the spot on the
ribbon closest to the alpha carbon (the "primary atom"). I can see how to do
this with the molecule attributes panel, but I'm having difficulty setting
the placement through the command line.

And while I'm at it...is there a way to color a spot on the ribbon closest
to the alpha carbon a different color than the rest of the ribbon?

Thanks for the help!


Daniel Gurnon, Ph. D.
Associate Professor of Chemistry
DePauw University
Greencastle, IN 46135

p: 765-658-6279
e: danielgurnon at depauw.edu
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