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Official Release PyMOL v1.8.4 has been released on October 4, 2016.
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
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Format bonds

Type Python Module
Author(s) Andreas Warnecke
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

The script format_bonds will automatically format bonds in amino acids.


format_bonds [ selection [, bonds ]]


import format_bonds

frag PHE

format_bonds bonds=2


  • Remember to correctly configure plugin import (see: Git intro)
  • format_bonds will introduce delocalized bonds by default or when bonds is larger than 2.
  • Setting bonds=1 will simply disable valence display (globally!)
  • The selection argument is 'all' by default and can be used to restrict editing to selected residues.
  • Note that format_bonds will also format acidic residues, the ..→
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