Generalized crystallography

X-ray crystal structure analysis can now be seen as a special kind of microscopy which is being extended to the recognition and examination of many kinds of ordered structure more general than crystals and which leads to their synthesis or construction by various methods. Electron microscopy and many other techniques now combine to give a coherent science of structure at the scale range of Ångstroms to microns, atoms to assemblies visible to the eye, which should continue to be called crystallography although it overlaps with nanotechnology, molecular biology, and solid state physics. Most generally, a crystal is a structure the description of which is much smaller than the structure itself and this view leads to the consideration of structures as carriers of information and on to wider concerns with growth, form, morphogenesis, and life itself

MCViNE -- An object oriented Monte Carlo neutron ray tracing simulation package

MCViNE (Monte-Carlo VIrtual Neutron Experiment) is a versatile Monte Carlo (MC) neutron ray-tracing program that provides researchers with tools for performing computer modeling and simulations that mirror real neutron scattering experiments. By adopting modern software engineering practices such as using composite and visitor design patterns for representing and accessing neutron scatterers, and using recursive algorithms for multiple scattering, MCViNE is flexible enough to handle sophisticated neutron scattering problems including, for example, neutron detection by complex detector systems, and single and multiple scattering events in a variety of samples and sample environments. In addition, MCViNE can take advantage of simulation components in linear-chain-based MC ray tracing packages widely used in instrument design and optimization, as well as NumPy-based components that make prototypes useful and easy to develop. These developments have enabled us to carry out detailed simulations of neutron scattering experiments with non-trivial samples in time-of-flight inelastic instruments at the Spallation Neutron Source. Examples of such simulations for powder and single-crystal samples with various scattering kernels, including kernels for phonon and magnon scattering, are presented. With simulations that closely reproduce experimental results, scattering mechanisms can be turned on and off to determine how they contribute to the measured scattering intensities, improving our understanding of the underlying physics.Comment: 34 pages, 14 figure

Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

The structure of protein molecules : in celebration of the International Year of Crystallography, 2014

Many people, including laymen, are aware of the double helical nature of the DNA molecule. A few may actually realise that it was the technique of X-ray crystallography that was the key to solving this structure. Even fewer will understand the uses and applications of crystallography to the most diverse of biological materials; proteins. In this review we discuss the application of a number of methodologies required to progress from a cloned gene to protein expression and purification, crystallisation conditions and eventually to X-ray structure determination. We provide our own experience in the field as examples of the procedures required. Protein crystallographers worldwide are contributing to our understanding of how enzymes work, how our immune system defends us against viruses and are using structural information to design novel pharmaceutical reagents.peer-reviewe