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@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@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@C1 :lig@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@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@C1 :lig@Cl1 Created 0 bonds
Il giorno mar 6 set 2022 alle ore 18:16 Elaine Meng <meng@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@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@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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