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

[Enrico Martinez]

P.S Assuming that I am running chimeraX from batch file, would it be
possible to script it a little bit to create the bond with the Cl1 and
the nearest carbon atom of the ligand (it may be C1, C2, C3, C4 etc
..) ?
Many thanks in advance
Enrico

Il giorno mar 6 set 2022 alle ore 18:33 Enrico Martinez
<jmsstarlight at gmail.com> ha scritto:
>
> 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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