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MacPyMOL is a Macintosh platform-specific Incentive Product for PyMOL subscribers.


The advantages of MacPyMOL over regular cross-platform PyMOL are:

  • A unified one-window interface.
  • Direct export of QuickTime movies.
  • Copy & paste support for images under Mac OS X.
  • X11 hybrid mode: Native OpenGL performance compatible with external Plugins.

X11 Hybrid Mode

The X11 Hybrid mode enables MacPyMOL to run open-source plugins and provides the same two-window interface found on Linux and Windows.

To use MacPyMOL in X11 Hybrid Mode, rename or copy the MacPyMOL executable to PyMOLX11Hybrid. At the command line, this can be done via


If using the Finder, simply duplicate the “MacPyMOL” icon to create “MacPyMOL Copy” and then rename “MacPyMOL Copy” to “PyMOLX11Hybrid”.

Note that X11 is required to run PyMOLX11Hybrid.


Since MacPyMOL is built on Apple's proprietary closed-source Cocoa platform, MacPyMOL is likewise a proprietary closed-source product.


MacPyMOL is fully compatible with Open-Source PyMOL, and session files written with one can be read with the other. Furthermore, in X11 Hybrid Mode, MacPyMOL can integrate the same open-source plugins as Open-Source PyMOL.

macpymol.txt · Last modified: 2013/08/19 21:01 (external edit)