Hi Eric,

OK. Turns out the problem only occurs when I build a single amino acid structure. Which, admittedly, would not be a residue.

Just FYI, I'm making a series of still images of single amino acids represented in different styles (ball and stick, etc), all with the same backbone orientation relative to the camera. I figured I would build the first one, set the phi and psi angles, orient the camera, and iterate through the remaining structures with swapaa. It occurs to me now that I could do this by simply hiding the second amino acid of a 2AA peptide, so I'll just do that. Thanks!

____________________________

Daniel Gurnon, Ph. D.

Associate Professor of Chemistry and Biochemistry

DePauw University

Greencastle, IN 46135

On Mon, Jul 20, 2026 at 2:33 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Dan,
I cannot reproduce this behavior. The following commands result in residue 2 of the built peptide being changed to lysine:

build start peptide "custom built" ASHNG -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack
select /A:2@O
swapaa sel LYS

Perhaps you could use Help→Report A Bug to submit a bug report about how to reproduce your problem….

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

On Jul 20, 2026, at 11:17 AM, Daniel Gurnon via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,
I occasionally use ChimeraX's "build structure" to construct short peptides to use in teaching. For efficiency's sake, it would be nice if I could take things I've already built and "mutate" an amino acid using the swapaa command. However, when I try to do this using a custom built structure (for example, selecting the residue I want to change, and then executing swapaa sel arg), I get the error "No amino acid residues specified for swapping".

The command works for downloaded structures, just not the custom ones. Is there a missing attribute that swapaa checks for, that isn't created when you make a custom peptide?

Dan
____________________________

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