Using Coot with PHENIX
- Reference
Coot 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
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 it is possible that your
installation is incomplete, but communication with Phenix will usually be
unaffected.
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.
Reference
- Emsley P, Cowtan K. Coot: model-building tools for molecular
graphics. Acta Cryst. 2004, D60:2126-32.
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