[Chimera-users] Delete pseudobonds

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 12 09:37:35 PDT 2018

Hi Javier,
You can delete it using the Pseudobond Panel (in menu under Tools… General Controls): click “missing segments” on the left to choose it, then click the “close” button on the right (different than the Close button at the bottom, which closes the panel).

However, this does not solve your problem:  Chimera already considers those atoms to be covalently bonded because of the CONECT records in your file, and will not let you add another bond.  The only reason it  was shown as a pseudobond instead of regular bond is that the distance was abnormally long (>3 A).

If you want to add a bond between the atoms you should remove the CONECT records from your PDB file before opening.  Then there will not be any covalent bond between the atoms yet, so you can select and bond them.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 12, 2018, at 1:34 AM, Javier Marchena <javier.mar97 at gmail.com> wrote:
> Hi,
> A pseudobond has been automatically created in one of my structures, because of "missing segments". I want to delete the pseudobond in order to create a real covalent bond between those two atoms. But I have problems with deleting the pseudobond, I have not found a way to do it. Could you help me out?
> Thanks in advance.
> PS: I send you the molecule in pdb format just for you to see the pseudobond.

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