Graphical interface. If you intend to use the graphical interface and installed Phenix using the Mac or Windows graphical installers, no further configuration is necessary - just double-click the icon for the main Phenix GUI. What is PHENIX b. A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. How to install PHENIX c. How to set up your environment to use PHENIX d. Running PHENIX e. The PHENIX Graphical User Interface f. The main modules in PHENIX g. The Graphical User Interface (GUI) to PHENIX is designed as a stand-alone object-oriented package that interfaces with the core PHENIX program modules. The graphical user interface (GUI) for phenix.refine. AFITT is tightly integrated to work with either REFMAC or PHENIX as refinement programs. Instructions below are for users of the command-line installer and/or programs. As input, only a PDB file and appropriate geometry restraints (in CIF format are required. (The geometry restraints are actually optional if you uncheck the box "Stop for unknown residues", but they are strongly recommended.) Instructions below are for users of the command-line installer and/or programs. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. Refine Complex: Refine Page¶. • Brief description of Phenix Graphical User Interface • Brief description of Phenix Programs covered in our Tutorial • Data analysis: Xtriage | Merging Statistics • Molecular Replacement: Phaser • Data and model visualization: Coot • Refinement: Phenix.refine • Miscellaneous: PDB Tools and Density modification [time permitting] If the refinement program is properly installed and the refinement workflow is set up, AFITT can launch it and validate its output. If you intend to use the graphical interface and installed Phenix using the Mac or Windows graphical installers, no further configuration is necessary - just double-click the icon for the main Phenix GUI. The phenix.refine graphical user interface (GUI) is integrated with Coot (Emsley et al., 2010) and PyMOL (DeLano, 2002), so that refined models and associated maps can be readily displayed and analyzed. The Graphical User Interface (GUI) to PHENIX is designed as a stand-alone object-oriented package that interfaces with the core PHENIX program modules. Running Phenix. Several hundred parameters enable extensive customizations for complex use cases. Essentially all of the program details described in this … This enables PHENIX to be used via the command line in situations where a graphical user interface is not required, but seamless used with the GUI when user interaction is required. It is primarily a frontend to the command line programs, with several extra graphical utilities for validation, map generation, and file … The Phenix graphical user interface (GUI) provides an intuitive way for researchers to perform crystallographic operations and to execute complex automated algorithms. While phenix.refine is the main crystallographic refinement program of Phenix, the following integrated alternatives exist. Running Phenix. The graphical interface for phenix.refine runs the unmodified command-line version; default settings are unchanged. Introduction to PHENIX a. phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. • Brief description of Phenix Graphical User Interface • Brief description of Phenix Programs covered in our Tutorial • Data analysis: Xtriage | Merging Statistics • Molecular Replacement: Phaser • Data and model visualization: Coot • Refinement: Phenix.refine • Miscellaneous: PDB Tools and Density modification [time permitting]

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