Detection and correction of underassigned rotational symmetry prior to structure deposition

An X-ray structural model can be reassigned to a higher symmetry space group using the presented framework if its noncrystallographic symmetry operators are close to being exact crystallographic relationships. About 2% of structures in the Protein Data Bank can be reclassified in this way

A robust bulk-solvent correction and anisotropic scaling procedure

A robust method for determining bulk-solvent and anisotropic scaling parameters for macromolecular refinement is described. A maximum-likelihood target function for determination of flat bulk-solvent model parameters and overall anisotropic scale factor is also proposed

Algorithms for deriving crystallographic space-group information. II. Treatment of special positions

Algorithms for the treatment of special positions in 3-dimensional crystallographic space groups are presented. These include an algorithm for the determination of the site-symmetry group given the coordinates of a point, an algorithm for the determination of the exact location of the nearest special position, an algorithm for the assignment of a Wyckoff letter given the site-symmetry group, and an alternative algorithm for the assignment of a Wyckoff letter given the coordinates of a point directly. All algorithms are implemented in ISO C++ and are integrated into the Computational Crystallography Toolbox. The source code is freely available

Exact direct-space asymmetric units for the 230 crystallographic space groups

A reference table of exact direct-space asymmetric units for the 230 crystallographic space groups is presented, based on a new geometric notation for asymmetric unit conditions

Automatic multiple-zone rigid-body refinement with a large convergence radius

Systematic investigation of a large number of trial rigid-body refinements leads to an optimized multiple-zone protocol with a larger convergence radius

Towards automated crystallographic structure refinement with phenix.refine

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. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods

On macromolecular refinement at subatomic resolution with interatomic scatterers

Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules

Robust indexing for automatic data collection

Improved methods for indexing diffraction patterns from macromolecular crystals are presented. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice

Surprises and pitfalls arising from (pseudo)symmetry

The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented