<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Oops, here is the picture I forgot to attach (not that it's terribly useful anyway)!<div class=""><br class=""></div><div class=""><img apple-inline="yes" id="7277DA5D-E95D-4AEF-A6DC-ACE5FD73C78E" src="cid:D92BA79F-9A8D-43CC-A025-71F26FCCB365" class=""><br class=""><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class="">On Sep 22, 2021, at 2:14 PM, Elaine Meng via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi Nicole,<br class="">You could just add a bond (after deleting any other atoms as needed to make a "vacancy" on the two atoms to be bonded). E.g. see attached picture from opening 1gcn, hiding ribbon, showing atoms, deleting one of the C-terminal carboxylate oxygens, and then adding a bond.<br class=""><br class="">open 1gcn<br class="">~ribbon<br class="">display<br class="">delete :29@oxt<br class="">bond :1@n:29@c<br class=""><br class="">Of course this could make a really bad structure with a ridiculous long bond, and minimization has only very limited ability to "rescue" such a thing. But maybe you were planning to do molecular dynamics or other modeling that might be able to work from that starting point. Or you could try rotating some of the backbone torsions before forming the bond to make it less ridiculous.<br class=""><br class="">See "modifying structures" page and links therein<br class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Sep 22, 2021, at 1:56 PM, Nicole Ostrovsky via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hello,<br class=""><br class="">I am trying to connect two sides of a peptide together to make it cyclic. Is there a way to do this that doesn't involve adding in another amino acid? I have been adding a glycine by individual atom using the modify structure tool but I'm wondering if I can do it a different way.<br class=""><br class="">Best,<br class="">Nicole Ostrovsky<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></blockquote><br class=""></div></div></div></body></html>