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| Python-based Hierarchical ENvironment for Integrated Xtallography |
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Using Coot with PHENIXInstructions for useCoot is an open-source (GPL) model-building program written by Paul Emsley. If a recent version of Coot (0.5 or later) with Python enabled is installed on your system, PHENIX can use it as a viewer for map and model files. The path to the Coot executable will be detected automatically if it is already part of the $PATH environment variable or is in one of several standard locations. If not, you will need to enter the path explicitly in the Preferences.  The main interface includes a button for launching Coot, and the Utilities menu in most programs contains a "Launch Coot" item. You must start Coot from within PHENIX for the programs to communicate; a single Coot window will be shared between all windows in a single instance of PHENIX. The Graphics pane of the Preferences dialog has an option to automatically start Coot whenever PHENIX is launched.  Once the Coot window appears, you should see additional buttons on the toolbar for toggling communication with PHENIX and showing/hiding hydrogen atoms. There will also be a new menu titled PHENIX. Currently this only enables launching of phenix.refine with an open model pre-loaded. If you do not see any modifications to the Coot window, you probably downloaded a version without Python (see "Common problems" below for details). As long as Coot is open, any PDB file can be viewed there by right-clicking the magnifying glass icon next to the file name and choosing "Open in Coot" from the menu that appears. If Coot is selected as the default PDB viewer (in Preferences->File Handling), you may simply left-click the icon. Most applications that output models and/or maps will display a button alongside the results that will load. the output file(s) in Coot. In the phenix.refine, AutoBuild, and AutoSol GUIs, the current model and maps will be automatically updated in Coot after every cycle of refinement or building. These models will be colored cyan and are regularly overwritten; use the yellow model if you want to make permanent changes. In phenix.refine, the start model will also be displayed (in purple). To disable these automatic updates, uncheck "Show progress in graphics window" in Preferences->Graphics. Most applications output either a simple F(obs) map (FP PHI FOM), often after density modification, or a pair of 2mFo-DFc and mFo-DFc difference maps. By default, the F(obs) and 2mFo-DFc maps will be contoured at 1 sigma (1 standard deviation above the mean) and colored blue, and the mFo-DFc map will be contoured at +/- 3 sigma and colored green and red. You can change these colors in the Preferences (Color section). Common problems
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