Install PyMOL

PyMOL is a user-sponsored molecular visualization system on an open-source foundation. Please support development of this open, effective, and affordable software by purchasing a subscription to maintenance and/or support. While a subscription to PyMOL gives access to pre-compiled binaries, you can freely download the latest source code tarball (version 1.4.1 as of June 20, 2011) here.
Once you have downloaded and unpacked PyMOL sources, cd into pymol to build the source code.

In the following links you will find instructions to build PyMOL from source on different platforms:

  Windows

  Linux

  Solaris x86

  FreeBSD

  Intel Mac OS X

After successfully installing PyMOL, you will need to move the PyMOL executable in your executable path, or update your PATH environment variable. Alternatively, you may point the O3_PYMOL environment variable to the PyMOL executable before running Open3DALIGN, or use the env pymol keyword in your Open3DALIGN script.