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Welcome To PyMOL

PyMOL is a capable molecular viewer and renderer. It can be used to prepare publication-quality figures, to share interactive results with your colleagues, or to generate pre-rendered animations. Nowadays, thousands of scientists around the world routinely rely upon PyMOL for such tasks.

Project Background

Where Does PyMOL Fit? (in relation to other tools)

PyMOL is primarily a figure, movie, and presentation generation tool. However, it can also be used for a variety of both routine and specialty tasks, such as visualization of electrostatic surface potentials and molecular dynamics trajectories.

With respect to figure making, PyMOL is an alternative to Molscript, BobScript, PovScript, and Raster3D. PyMOL's primary advantage over these packages is the ability to use a graphical user interface instead of (or in addition to) command-line scripts.

With respect to movie generation, PyMOL can create and output 3D molecular movies in much the same way these others tools do for general 3D animations Maya, Blender, Cinema4D, and 3ds Max. PyMOL can also be used to generate geometric inputs for use with these general-purpose animation tools.

With respect to presentations, PyMOL works like an animated 3D molecular PowerPoint in that PyMOL Sessions (analogous to PowerPoint PPT files) can be constructed using a sequence of Scenes (analogous to PowerPoint Slides) which smoothly flow from one into another to communicate results or tell stories.

What are PyMOL's Strengths and Weaknesses?


  • Graphics Quality: A built−in ray tracer gives you shadows and depth on any scene. You can also render externally.
  • Movies: Creating movies can be as simple as loading multiple PDB files and hitting play.
  • Output Options: Images can be copied & pasted directly into PowerPoint and Keynote. Static images and rendered sequences can be output in PNG format, and as QuickTime movies (on Mac OS X).
  • Atom Selections: Arbitrary logical expressions facilitate focused visualization and editing.
  • Surface renditions: As good if not better than Grasp, and mesh surfaces are supported too.
  • Cartoon renditions: PyMOL's cartoons are almost as nice as Molscript but are much easier to create and render.
  • Command−Line and GUI Control: Complex “real world” applications often require both.
  • Molecular Splits/Joins: Structures can be sliced, mutated, and reassembled on the fly and written out to standard files (i.e. PDB, MOL/SDF).
  • Scripting: One of the best ways to control PyMOL is through reusable scripts, which can be written in the command language or in Python.
  • Conformational Editing: Click and drag interface allows you to edit conformations naturally. Sculpting allows the molecule to adapt to your changes.
  • Expandability: The PyMOL Python API provides a solid way to extend and interface.
  • Cross−Platform Code: A single code base supports both Unix, Macintosh, and Windows, using OpenGL and Python and a small set of Open−source external dependencies.


  • User Interface: Development has mostly been focused on capabilities, not on ease−of−use for new users.
  • Documentation: Weak, but improving.
  • Object−Orientation: There is a single monolithic, command-oriented programming interface.

Is PyMOL Free?

Yes, but…

PyMOL is Copyrighted software freely available as “Open Source” source code. This means that so long as you compile the program from source code, you may use, modify, and redistribute the resulting executables without paying fees or infringing Copyrights. Thus you can be confident that the time you invest today in learning the package will provide you with long term utility no matter where your career happens to take you. You will never be required to pay software license fees to use Open-Source PyMOL or to share it with others.

Nevertheless, PyMOL is not free to develop, document, maintain or support. So if you adopt the software, you are expected to contribute to the project in some manner. Although such contributions may take a variety of forms, most contributors choose to sponsor the project by purchasing a PyMOL Maintenance Subscription in order to get access to the latest precompiled PyMOL builds as well as this official documentation site.

All PyMOL Subscriptions include access to the official PyMOL builds for the Windows, Mac OS X, and Linux operating systems, and all include access to this documentation site.

Where is PyMOL Going?

No one can know the future for certain, but it is likely that PyMOL will continue to evolve in a manner directly reflective of the needs of its major sponsors and heaviest users, who provide the means and impetus. Thus, if you want something specific from PyMOL in the future, please make your wishes known, and back them up with whatever resources you can muster.

Generally speaking, we anticipate expanded capabilities in terms of animation, illustration, and communications, targeting both computational chemistry and structural biology data sources. PyMOL continues to see heavy usage as a vehicle for sharing molecular information between teams, so it is reasonable to expect additional features in the area. Demand from integration with established commercial packages (e.g. MOE and Maestro) remains strong, so more formats are likely to be supported over time. Finally, there is still much desire expressed for integrated building and modeling capabilities, so those wishes will likely be met eventually as well, though most likely through integration of third-party products.

welcome.txt · Last modified: 2013/08/19 21:00 (external edit)