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

[Elaine Meng]

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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