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News & Updates
Official Release PyMOL v2.0 has been released on September 20, 2017.
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
Official Release PyMOL v1.8.6 has been released on March 9, 2017.
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.
Older News See Older News.
Did you know...


Flag is a command to set or clear flags on atom sets. A flag is just some atom-specific property. A flag is either on or off for a residue. Possible flags are:

  • Flags 0-7 are reserved for molecular modeling

focus = 0

Atoms of Interest (i.e. a ligand in an active site)

free = 1

Free Atoms (free to move subject to a force-field)

restrain = 2

Restrained Atoms (typically harmonically constrained)

fix = 3

Fixed Atoms (no movement allowed)

exclude = 4

Atoms which should not be part of any simulation
  • Flags 8-15 are free for end users to manipulate
  • Flags 16-23 are reserved for external GUIs and linked applications
  • Flags 24-30 are reserved for PyMOL internal usage

exfoliate = 24

Remove surface from atoms when surfacing


Ignore atoms altogether when surfacing

no_smooth = 26

Do not smooth atom position
  • Flag 31 is reserved for coverage tracking when assigning parameters, etc.

If the 'auto_indicate_flags' setting is true, then PyMOL will ..→

A Random PyMOL-generated Cover. See Covers.