[Chimera-users] Making and Breaking bonds in Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 4 10:03:13 PDT 2005

Hi David,
See the command bond, plus the "see also" commands in its man page:


If you didn't want to type the atom names, you can select the two atoms 
and then use

bond sel
(to create the bond)
~bond sel
(to delete the bond)

An approach with the menu is to select the bond (but not the flanking 
atoms) and then use Actions... Atoms/Bonds... delete

Another way to add bonds is to add CONECT lines to the PDB file, but 
then you have to put in CONECT lines for that whole residue, and it can 
get complicated.
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 4, 2005, at 8:25 AM, David Chenoweth wrote:

> Dear Chimera users,
> Does anyone know how to make a new bond or delete a bond between two 
> atoms within a PDB file using chimera?
> -Thanks
> DC

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