[Chimera-users] Adding New Covalent Bond?

[Elaine Meng]

> On May 26, 2020, at 9:52 AM, Ammar Jastaniah <ajasta2 at uic.edu> wrote:
> 
> Hi Elaine,
> Is there any way to connect/make new bonds between adjacent, somewhat distant carbon atoms within a ligand structure (perhaps still using the 'Build Structure' feature)?
> Thank you.
> Ammar 

Hi Ammar,
Assuming this is a Chimera question (we are now developing ChimeraX) the answer is yes, in the Adjust Bonds section of Build Structure, you can choose to add a bond between any two selected atoms regardless of the distance between them.  Just choose the "all possible" option.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

Or, you could use the "bond" command:  <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>

The chimera-users at cgl.ucsf.edu address (CC'd here) is recommended for Chimera questions, unless private data are included.

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