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It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation calledDiSCaMB, `densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed,DiSCaMBis an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

The foundations and current features of a widely used graphical user interface for macromolecular crystallography are described., A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified.

Application of phenix.model_vs_data to the contents of the Protein Data Bank shows that the vast majority of deposited structures can be automatically analyzed to reproduce the reported quality statistics. However, the small fraction of structures that elude automated re-analysis highlight areas where new software developments can help retain valuable information for future analysis., phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed.

Systematic investigation of a large number of trial rigid-body refinements leads to an optimized multiple-zone protocol with a larger convergence radius., Rigid-body refinement is the constrained coordinate refinement of one or more groups of atoms that each move (rotate and translate) as a single body. The goal of this work was to establish an automatic procedure for rigid-body refinement which implements a practical compromise between runtime requirements and convergence radius. This has been achieved by analysis of a large number of trial refinements for 12 classes of random rigid-body displacements (that differ in magnitude of introduced errors), using both least-squares and maximum-likelihood target functions. The results of these tests led to a multiple-zone protocol. The final parameterization of this protocol was optimized empirically on the basis of a second large set of test refinements. This multiple-zone protocol is implemented as part of the phenix.refine program.

Details are described of the calculation of new parallelity restraints recently introduced in cctbx and PHENIX., Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox (cctbx) are presented.