If you have ISOLDE installed, it also provides a tool to automatically form all “reasonable” (based on geometry) disulfides in a model. It’s not currently provided as a command, but it’s automatically run whenever you choose a model for ISOLDE to work on (it will bring up a dialogue box asking for confirmation if it finds anything).
Hello Vladimir,
Yes, you can add a bond between two atoms. First show the atoms, then select the two that you want to bond (Ctrl-click on one, Shift-Ctrl-click on the second one so that both are highlighted in green), and then either
(1) use the "bond" command, e.g. if the two atoms are selected you can specify them with "sel":
bond sel
If the atoms are deemed to be too far apart you may need to include "reasonable false" to make the bond anyway, see the help:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
- or -
(2) use the Build Structure tool, the Adjust Bonds section (menu: Tools... Structure Editing... Build Structure)
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds>
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco
> On Jun 2, 2023, at 11:58 AM, Vladimir Saudek via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
>
> Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file?
>
> Thank you
>
> Vladimir
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