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. Author manuscript; available in PMC: 2012 Sep 1.
Published in final edited form as: Methods. 2011 Jul 29;55(1):94–106. doi: 10.1016/j.ymeth.2011.07.005

Figure 2.

Figure 2

Integration of refinement and validation with model rebuilding in Coot[31]. After refinement or structure validation is finished the current model and electron density maps are displayed in Coot, information being transferred between Phenix and Coot using Python and the XML-RPC communication protocol. The validation lists in Phenix are interactive, for example, clicking on a rotamer outlier in the rotamer list will re-centre the Coot display to that rotamer. Other validation information, such as the contacts between atoms calculated with the Probe program, are also automatically displayed in Coot.