[chimerax-users] Visualization of the carbon - Cl bond in a small molecule

[Elaine Meng]

Hello,
Maybe the distance was longer than what ChimeraX thinks is a bond.  Anyway, if the bond is missing you can add it with the "bond" command (or if you prefer GUI, with Tools... Structure Editing... Build Structure tool, Adjust Bonds section).

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>

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




> On Sep 6, 2022, at 8:34 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users!
> I have an issue with the visualization of the small molecule obtained
> from the tleap module of the amber tools. First of all in vmd and
> pymol everything looks OK. In the ChimeraX there is no bond between
> atom CL of the ligand and the aromatic C atom. I've tried to change
> atom type for the CL:
> setattr :lig at CL1 atoms idatm_type CL
> show :lig@*
> 
> but the bond is still absent. Would it be possible to rebuild it manually?
> Cheers,
> Enrico