Installing Phenix and CCTBX on OS X
From OS X Scientific Computing
Phenix (Python-based Hierarchical Environment for Integrated Xtallography) is a new macromolecular crystallography software package being developed with automation in mind.
It has a GUI that is now available not only in the Linux version, but also OS X. (So much of the stuff below should be regarded as optional or obsolete. I'll leave it in place for awhile ....
It has command-line utilities, called cci_apps, that can be compiled on OS X (and are currently also distributed in binary form for 10.3.9 ppc). Phenix and its command-line utilities are, like CNS, restricted to nonprofit users, and you need to register for and download the software. For that reason, there is no official fink package for cci_apps, but I have made a fink install script that enables you to install cci_apps using fink. It is also very easy to install this manually in (eg) /usr/local. These options are described on the first linked page below.
Phenix in turn is based on a genuinely open-source component, called cctbx. For that reason, you can install it without restriction, using either fink or from a precompiled binary available on their page. This is described in more detail on the page linked below.
The elbow.builder module of phenix is especially nice for creating cif and pdb files for weird or nonstandard ligands. Often this can be done with a standard pdb file of the molecule, but if you don't have one (you are starting with only a chemical structure drawing, for example) you can use elbow.builder with SMILES strings to generate everything.