Alexandre Urzhumtsev

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.

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

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.

FEM: Feature-enhanced map

The non-iterative feature-enhancing approach improves crystallographic maps’ interpretability by reducing model bias and noise and strengthening the existing signal.

Crystallographic model quality at a glance

The representation of crystallographic model characteristics in the form of a polygon allows the quick comparison of a model with a set of previously solved structures.

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.

Bulk-solvent and overall scaling revisited: faster calculations, improved results

A fast analytical method for calculating mask-based bulk-solvent scale factors and overall anisotropic correction factors is introduced.

Real-space refinement in PHENIX for cryo-EM and crystallography

A description is provided of the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite and its application to the re-refinement of cryo-EM-derived models.

On the use of logarithmic scales for analysis of diffraction data.

Conventional and free R factors and their difference, as well as the ratio of the number of measured reflections to the number of atoms in the crystal, were studied as functions of the resolution at which the structures were reported. When the resolution was taken uniformly on a logarithmic scale, the most frequent values of these functions were quasi-linear over a large resolution range.

A program to analyze the distributions of unmeasured reflections

Crystallographic Fourier maps may contain barely interpretable or non-interpretable regions if these maps are calculated with an incomplete set of diffraction data. Even a small percentage of missing data may be crucial if these data are distributed non-uniformly and form connected regions of reciprocal space. Significant time and effort can be lost trying to interpret poor maps, in improving them by phase refinement or in fighting against artefacts, whilst the problem could in fact be solved by completing the data set. To characterize the distribution of missing reflections, several types of diagrams have been suggested in addition to the usual plots of completeness in resolution shells and cumulative data completeness. A computer program, FOBSCOM, has been developed to analyze the spatial distribution of unmeasured diffraction data, to search for connected regions of unmeasured reflections and to obtain numeric characteristics of these regions. By performing this analysis, the program could help to save time during structure solution for a number of projects. It can also provide information about a possible overestimation of the map quality and model-biased features when calculated values are used to replace unmeasured data.

Cluster analysis for phasing with molecular replacement: a feasibility study

Molecular replacement with the simultaneous use of several search functions may solve the phase problem when the conventional molecular-replacement procedure fails to identify the solution.