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

[Enrico Martinez]

Thank you very much Elaine!
Actually I have already tried bond command but it didn't work for this
structure:
bond :lig at C1 :lig at Cl1
Created 0 bonds

Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng
<meng at cgl.ucsf.edu> ha scritto:
>
> 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
>