Python-based Hierarchical ENvironment for Integrated Xtallography

Instructions for installing external software interfacing with PHENIX

Coot

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Coot is the standard programfor model-building into density, written chiefly by Paul Emsley. Theextensions included with the PHENIX GUIallow control of Coot from PHENIX, including automatic loading of models andmaps. This requires a build of Coot that includes a working Pythoninterpreter; if the PHENIX extensions are not functioning, this is almostcertainly due to the lack of Python in the Coot build. Note: the installersavailable on the CCP4 web page have not worked with PHENIX in the past; asof May 2011, the Mac installer appears to be fine, but you will need to specifythe path (/Applications/coot.app) in the PHENIX preferences.

For Linux:
We recommend downloading installers directly fromPaulEmsley's web page. Any file with 'python' in the name is suitable for usewith PHENIX. Most of these will work on other OSes than those named, but wehaven't tested them extensively.
For Mac:
Two options are available: use the Finkpackage manager, or download a standalone installation. Both aredescribed on Bill Scott's web page. Note that you will need to berunning Snow Leopard (OS 10.6) to use many of these, but some obsolete (butstill functional) builds of Coot for older OSes are available. The builds arenow nightly, and include both command-line and graphical installers. For older versions ofMac OS (10.4 or 10.5), the more recent packages do not work with PHENIX, soyou will need to use the obsoleteCoot 0.6 build.

Coot Download Linux

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 inPreferences->Graphics->Full path to Coot. A few specific paths are searchedautomatically. On Mac, most installations should be automatically detected,but you may need to set the path explicitly to ensure that the correct versionis used.

PyMOL

PyMOL is a popular open-source moleculargraphics program, written by the late Warren DeLano and now maintained bySchrodinger. We distribute anobsolete binary build of PyMOL (version 0.99) with PHENIX, but this islacking some significant features and we recommend that you use the newestrelease. A variety of options are available for both Linux and Mac, includinginstallation via some package managers (Fink, and some Linux distributions),custom installation from source, or proprietary builds (with additionalfeatures) purchased from Schrodinger. Either open-source or proprietaryversions should work well with PHENIX. (We mostly test with MacPyMOL version1.2.)

Coot Model Building

As with Coot, you may have to point PHENIX to the PyMOL executable (inPreferences->Graphics->Full path to PyMOL) if it is not found automatically.On Mac, it will use /Applications/MacPyMOL.app if present.

Download Coot For Mac