On the systematic scaling and merging of multiple datasets in macromolecular crystallography
James Foadi, Yilmaz Alguel, Wesley Armour, D. Axford, A. Cameron, Robin Leslie Owen, David Geoffrey Waterman, Gwyndaf Evans · Acta Crystallographica Section A Foundations of Crystallography · 2011
Microsymposia C162are primarily command-line driven, an emphasis has been placed on ease-of-use and automation.We have developed a graphical interface for the major components of PHENIX, which currently includes phenix.refine, phenix.xtriage,comprehensive validation tools based on the Molprobity web server, Phaser, and the AutoSol, AutoBuild, AutoMR, and LigandFit automation "wizards".The Python-based framework allows new GUIs to be generated semi-automatically while preserving all of the flexibility of the command-line programs, and supports both Macintosh and Linux.Python extensions for Coot and PyMOL facilitate real-time visualization of refinement and automated model-building, and convenient viewing of results.Transitions between separate modules within PHENIX are simplified or eliminated in the GUI, reducing the amount of manual input required and avoiding the use of command-line tools.Further automation is possible with definition of standard parameter sets and input files for individual programs.Future improvements will include greater use of multiprocessing and clusters, tools for handling multiple structures in parallel, and new automation pipelines.