using swapaa with custom built peptides
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
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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Yeah, a limitation of the current swapaa implementation is that it only works on peptide chains, not isolated amino acids. —Eric
On Jul 20, 2026, at 12:07 PM, Daniel Gurnon via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 <mailto: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 <mailto: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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
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Daniel Gurnon -
Eric Pettersen