An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

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A short history of SHELX

SIR2004 is the evolution of the SIR2002 program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003). J. Appl. Cryst. 36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented in SIR2004 make this program efficient: it is able to solve ab initio both small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 A, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

SIR2004: an improved tool for crystal structure determination and refinement

In this review the phenomenon of proton conductivity in materials and the elements of proton conduction mechanismsproton transfer, structural reorganization and diffusional motion of extended moietiesare discussed with special emphasis on proton chemistry. This is characterized by a strong proton localization within the valence electron density of electronegative species (e.g., oxygen, nitrogen) and self-localization effects due to solvent interactions which allows for significant proton diffusivities only when assisted by the dynamics of the proton environment in Grotthuss and vehicle type mechanisms. In systems with high proton density, proton/proton interactions lead to proton ordering below first-order phase transition rather than to coherent proton transfers along extended hydrogen-bond chains as is frequently suggested in textbooks of physical chemistry. There is no indication for significant proton tunneling in fast proton conduction phenomena for which almost barrierless proton transfer is suggest...

Proton Conductivity: Materials and Applications

Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0–3.5 A, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package.

Substructure solution with SHELXD.

Computer and Robot Vision Vol. 1, by R.M. Haralick and Linda G. Shapiro, Addison-Wesley, 1992, ISBN 0-201-10887-1.

Computer and Robot Vision

Preface 1 Introduction 2 Tools for Solving the Phase Problem 21 Mathematical Methods 22 Computational Methods 23 Experimental Methods 3 Applications of Direct Methods to Macro-Molecular Structures 31 Integration of Direct Methods with Experimental Phase Information 32 Combining Direct Methods with Structural Information 33 Ab Initio Phasing 4 Latest Developments Index

Direct methods for solving macromolecular structures

Macromolecular crystallization in a high throughput laboratory—the search phase

An investigation of the homolytic dissociation of [.eta.5-C5Me5Cr(CO)3]2 and related complexes. The role of ligand substitution on the solution thermochemistry of metal-metal bond cleavage

Current structural genomics projects are likely to produce hundreds of proteins a year for structural analysis. The primary goal of our research is to speed up the process of crystal growth for proteins in order to enable the determination of protein structure using single crystal X-ray diffraction. We describe Max, a working prototype that includes a high-throughput crystallization and evaluation setup in the wet laboratory and an intelligent software system in the computer laboratory. A robotic setup for crystal growth is able to prepare and evaluate over 40 thousand crystallization experiments a day. Images of the crystallization outcomes captured with a digital camera are processed by an image-analysis component that uses the two-dimensional Fourier transform to perform automated classification of the experiment outcome. An information repository component, which stores the data obtained from crystallization experiments, was designed with an emphasis on correctness, completeness, and reproducibility. A case-based reasoning component provides support for the design of crystal growth experiments by retrieving previous similar cases, and then adapting these in order to create a solution for the problem at hand. While work on Max is still in progress, we report here on the implementation status of its components, discuss how our work relates to other research, and describe our plans for the future.

Intelligent decision support for protein crystal growth

Combined x-ray crystallographic, single-crystal EPR, and theoretical study of metal-centered radicals of the type [.eta.5C5R5Cr(CO)2L] (R = H, Me; L = CO, tertiary phosphine)

Suzanne Fortier

Papers

Direct methods for solving macromolecular structures

Macromolecular crystallization in a high throughput laboratory—the search phase

An investigation of the homolytic dissociation of [.eta.5-C5Me5Cr(CO)3]2 and related complexes. The role of ligand substitution on the solution thermochemistry of metal-metal bond cleavage

Intelligent decision support for protein crystal growth

Combined x-ray crystallographic, single-crystal EPR, and theoretical study of metal-centered radicals of the type [.eta.5C5R5Cr(CO)2L] (R = H, Me; L = CO, tertiary phosphine)