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

[Enrico Martinez]

Great, thank you very much!
It works!
Cheers,
Enrico

Il giorno mar 6 set 2022 alle ore 18:26 Elaine Meng
<meng at cgl.ucsf.edu> ha scritto:
>
> As mentioned in the help, there is a "reasonable false" option to add bond even if distance seems too long; try that:
>
> bond :lig at C1 :lig at Cl1 reasonable false
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html>
>
> > On Sep 6, 2022, at 9:22 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> >
> > 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
> >>
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