[Chimera-users] question on cyclization of peptide

[Elaine Meng]

Hi Jesse,
We're glad Chimera has been useful in your work!

Yes, this could be done in Chimera.  It may take several steps, however, to delete extra atom(s), add the bond to form the cycle, and minimize.  You might also want to rotate torsions interactively to put the ends in a more reasonable bonding distance before forming the bond.

The Build Structure tool (in menu under Tools...Structure Editing)
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

...includes the sections:

Start Structure - you can create the linear version of the peptide if you don't have it already.  Choose the "peptide" option and proceed from there.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>

Adjust Torsions - rotate torsions interactively to change conformation of your linear peptide
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>

...before adding the bond you may need to delete any extra atoms, i.e. if you used Start Structure to create the peptide, there will be an extra oxygen named OXT on the C-term end.  It could be deleted with command: delete @OXT

Adjust Bonds - add the bond: select the N-term N (Ctrl-click) and the C-term carbonyl C (Shift-Ctrl-click to add to the existing selection instead of erasing it) and then click to "Add" "all possible" bonds between selected atoms.  Choosing "all possible" instead of "reasonable" is probably required since the bond length may be longer than is reasonable, at this stage. (Or instead of the Adjust Bonds GUI, you could use command: bond sel )
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

Then you could try minimizing the cyclic peptide to make it less distorted, if needed.  Menu:  Tools.. Structure Editing... Minimize Structure. Click through the dialogs to add hydrogens and assign charges.  You may need to increase number of steps (e.g. 1000 steepest descent).
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.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 Mar 15, 2022, at 10:01 AM, JESSE JAYNES via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Folks,
> I have greatly appreciated the access to Chimera, thank you.  I need to generate a pdb of a cyclized version of linear 10mer peptide.  Is that possible to do in Chimera?
> Thank you,
> Jesse