The bonds are initially generated based on proximity between the atoms
in the structure.
To remove the erroneously generated bonds use command Unbond:
unbond atom1,atom2
04.06.2019 3:46, pymol-users-requ...@lists.sourceforge.net пишет:
Message: 1
Date: Mon, 3 Jun 2019 16:15:33 -0400
From: Hao
Here is one way to do this:
change your mouse mode from “viewing” to “editing”.
left-click on the atoms at each end of the bond you wish to remove,
each atom will highlight with a gray ball around it,
In the command line type "unbond pkset” and hit the enter key,
your bond will be removed.
> On Ju
Dear users,
I am working on a structure of a protein-ligand complex, and the ligand
contains an azetidine group. Whenever I display this structure in pymol, an
unwanted bond forms between 2 carbon atoms in the azetidine ring.
The pdb file of this ligand was generated by Chem3D and the restraint c
Dear Pymol users,
I am trying to generate the electrostatic
potential surface for my protein using the APBS plugin in Pymol. I
installed "ver 1.8.4.0" through the per-compiled binary using "apt-get"
in Ubuntu 18.04.2 LTS".
I am encountering the following error whi
