|Python-based Hierarchical ENvironment for Integrated Xtallography|
Coot is the standard program for model-building into density, written chiefly by Paul Emsley. The extensions included with the PHENIX GUI allow control of Coot from PHENIX, including automatic loading of models and maps. This requires a build of Coot that includes a working Python interpreter; if the PHENIX extensions are not functioning, this is almost certainly due to the lack of Python in the Coot build. Note: the installers available on the CCP4 web page have not worked with PHENIX in the past; as of May 2011, the Mac installer appears to be fine, but you will need to specify the path (/Applications/coot.app) in the PHENIX preferences.
To run Coot from the PHENIX GUI, you will either need to have the 'coot' executable somewhere in your shell's searchpath, or enter it in Preferences->Graphics->Full path to Coot. A few specific paths are searched automatically. On Mac, most installations should be automatically detected, but you may need to set the path explicitly to ensure that the correct version is used.
PyMOL is a popular open-source molecular graphics program, written by the late Warren DeLano and now maintained by Schrodinger. We distribute an obsolete binary build of PyMOL (version 0.99) with PHENIX, but this is lacking some significant features and we recommend that you use the newest release. A variety of options are available for both Linux and Mac, including installation via some package managers (Fink, and some Linux distributions), custom installation from source, or proprietary builds (with additional features) purchased from Schrodinger. Either open-source or proprietary versions should work well with PHENIX. (We mostly test with MacPyMOL version 1.2.)
As with Coot, you may have to point PHENIX to the PyMOL executable (in Preferences->Graphics->Full path to PyMOL) if it is not found automatically. On Mac, it will use /Applications/MacPyMOL.app if present.