Hi Jesse, The general peptide-building tool only includes standard amino acids (Tools... Structure Editing... Build Structure, then in that tool, go to the Start Structure section and choose peptide). <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start> However, you could build the O positions as K (lysine) instead, and then delete the sidechain N from each, and then using the Modify Structure section of the Build Structure tool, change the C next to it to N (tetrahedral with + charge, presumably). I think that makes ornithine, since it's like lysine except with one less CH2 in the sidechain. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#modify> <https://en.wikipedia.org/wiki/Ornithine> Or, if you have the swisssidechain plugin to Chimera that includes nonstandard amino acids, you may be able to use that plugin to swap the lysines with ornithines. <https://swisssidechain.ch/visualization/chimera.php> Its database includes ornithine (ORN): <https://swisssidechain.ch/browse/family/table.php?family=all> As for ChimeraX, it has the same peptide-building and structure-modifying capabilities as Chimera, but there is no plugin that provides the nonstandard amino acids currently. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 23, 2024, at 6:41 AM, Jessie Jaynes via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Folks,

I have a short peptide (O=ornithine)

FEFOGGOFEF

Is it possible to construct this peptide in Chimera?

Thank you, Jesse