Construction or refinement of approximate reduced density matrices
Jean‐Michel Gillet, P. Becker, Blandine Courcot, S. Ragot · Acta Crystallographica Section A Foundations of Crystallography · 2005
MICROSYMPOSIA C82algorithms for the determination of substructures (phenix.hyss), the refinement of macromolecular structures (phenix.refine),and the underlying "hybrid" open-source software framework, cctbx.The Phenix Hybrid Substructure Solution (phenix.hyss)combines Patterson methods and dual-space direct methods, automatic substructure comparisons and simple substructure refinement into a highly integrated algorithm.The Phenix refinement tools include Cartesian dynamics simulated annealing, a novel robust bulk-solvent correction procedure including overall anisotropic scaling, maximum likelihood refinement with and without experimental phases, and isotropic and anisotropic refinement of displacement parameters.Both phenix.hyssand phenix.refineare designed to minimize the need for tedious and error-prone manual intervention.Development of the required tools is made practical by the tight integration of a scripting language (Python) with a compiled language (C++), and maximization of source code reuse through a library-based approach.