A reader sent me a link to a posting on the brilliant Crystallography on OS X website highlighting the availability of a stand alone version of Coot for Mac OSX

With considerable help from Nat Echols, we can now build coot automatically every night a new revision is available. I have two versions, built on two different computers. The 10.6 version should run on 10.6.8 or greater. The 10.9 version is for 10.9 or later.. The package installer will install everything in /Library/Coot. Unfortunately, it breaks if you move it. A wrapper shell script called "coot" will reside in /usr/local/bin/coot when you are done.

Coot (Crystallographic Object-Oriented Toolkit) is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data.

Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

I've also added a link on the Spectroscopy page.