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Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch
News & Updates
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.4 have all been released on December 3, 2014.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.2 have all been released on August 4, 2014.
Official Release PyMOL, AxPyMOL, and JyMOL v1.7 have all been released today, January 14, 2014.
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.
New Plugin GROMACS_Plugin is a new plugin that ties together PyMOL and GROMACS.
New Software CMPyMOL is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
New Script cgo_arrow draws an arrow between two picked atoms.
Tips & Tricks Instructions for generating movie PDFs using .mpg movies from PyMOL.
Older News See Older News.
Did you know...


= Overview =

Vina is a new, very fast, molecular docking program, written by Oleg Trott. In order to run Vina, you should have MGLTools1.5.4 installed (you need and But, you don't need MGLTools for this script to run.

To run Vina it needs to know the center of the protein and also its extents (size in XYZ directions). We can easily do this with PyMOL.


  • COM -- simple script to get the center of mass of a selection


  • Commandline options
  • Robustness to vagaries of input
  • Usage & Help


pymol -cq ./ proteinFile ligandFile

For high-throughput screening, where we compare each ligand to each protein, I typically wrap the script in a for-loop like:

# foreach protein in my proteins directory
for protein in proteinsDir/*; do
  # foreach ligand in my ligands directory
  for ligand in ligandsDir/*; do;
    # make a  [[MakeVinaCommand|..→]]
A Random PyMOL-generated Cover. See Covers.

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