[Chimera-users] selection of specific bonds

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 11 09:34:41 PST 2019

Hi Damien,
You’ll like this… simply the command:  select carbonyl

It selects the atoms as well as the bond between them.

You can specify in the command line any of the functional groups that appear in the menu under Select… Chemistry… functional group.  It’s mentioned here:

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

> On Dec 11, 2019, at 8:02 AM, Damien Larivière <damien at fourmentinguilbert.org> wrote:
> Dear All,
> My question is naive but I have difficulties to figure out how to do it with Chimera.
> I would like to select specifically the group of two atoms (C and O) formed in a carbonyl bond C=O for all, say, GLU residues of a protein.
> Is there a way, via a command line, to do it?
> Thanks for your help on this.
> Damien

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