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News & Updates
Official Release PyMOL v1.8.2 has been released on April 20, 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.