Here are some quick notes on installing PyMol in OSX Mountain Lion using MacPorts:

1- First install Xquartz, which is basically X11 for OSX 10.8.

2- Install PyMol using MacPorts:

sudo port install tcl -corefoundation +threads
sudo port install tk -quartz +x11
sudo port install pymol-devel

# PyMol will be installed here:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymol

Note that MacPorts might not create the symbolic link for launching PyMol (which is basically __init__.py in the installation folder). So make an alias/link for it and remember to launch it using `/opt/local/bin/python2.7 (if it is not your default python).

This currently installs PyMol 1.5. You can also compile the latest version of PyMol (as of now 1.6 alpha) by downloading it and then using:

sudo /opt/local/bin/python2.7 setup.py install --home=~

This creates “bin” and “lib” directories in your home folder and then installs PyMol there.

[ Originally published here. ]