[Chimera-users] Connecting ends of a peptide

[Elaine Meng]

Hi Nicole,
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.

open 1gcn
~ribbon
display
delete :29 at oxt
bond :1 at n:29 at c

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.

See "modifying structures" page and links therein
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 22, 2021, at 1:56 PM, Nicole Ostrovsky via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello,
> 
> 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.
> 
> Best,
> Nicole Ostrovsky