If you install PyMol from MacPorts you may encounter the following: the control window does not work properly  or does not appears at all. You can save a little of Google diving if you make sure to build tcl (whitout core foundations) and tk (without xquartz) BEFORE trying to install pymol. Hence, you can save time if you follow these simple commands:

% sudo port install tcl -corefoundation
% sudo port install tk -quartz
% sudo port install pymol

This way you should get a fully functional OpenSource PyMol, althought problems related to other packages have been also reported. For additional reference this is the ticket entry at the MacPorts project webpage:

https://trac.macports.org/ticket/43482

I hope it helps

Jordi