Showing papers in "Journal of Applied Crystallography in 2012"
TL;DR: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF.
Abstract: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.
9,479 citations
TL;DR: The paper presents new developments and amendments to the ATSAS package (version 2.4) for processing and analysis of isotropic small-angle scattering data.
Abstract: New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.
1,634 citations
TL;DR: Nika is an Igor Pro-based package for correction, calibration and reduction of two-dimensional area-detector data into one-dimensional data (`lineouts'), open source and highly flexible.
Abstract: Nika is an Igor Pro-based package for correction, calibration and reduction of two-dimensional area-detector data into one-dimensional data (`lineouts'). It is free (although the user needs a paid license for Igor Pro), open source and highly flexible. While typically used for small-angle X-ray scattering (SAXS) data, it can also be used for grazing-incidence SAXS data, wide-angle diffraction data and even small-angle neutron scattering data. It has been widely available to the user community since about 2005, and it is currently used at the SAXS instruments of selected large-scale facilities as their main data reduction package. It is, however, also suitable for desktop instruments when the manufacturer's software is not available or appropriate. Since it is distributed as source code, it can be scrutinized, verified and modified by users to suit their needs.
768 citations
TL;DR: SIR2011, the successor of SIR2004, is the latest program of the SIR suite and can solve ab initio crystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data.
Abstract: SIR2011, the successor of SIR2004, is the latest program of the SIR suite. It can solve ab initio crystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities: e.g. a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometry via simulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.
522 citations
TL;DR: In order to address the specific needs of the emerging technique of `serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created.
Abstract: In order to address the specific needs of the emerging technique of `serial femtosecond crystallography', in which structural information is obtained from small crystals illuminated by an X-ray free-electron laser, a new software suite has been created. The constituent programs deal with viewing, indexing, integrating, merging and evaluating the quality of the data, and also simulating patterns. The specific challenges addressed chiefly concern the indexing and integration of large numbers of diffraction patterns in an automated manner, and so the software is designed to be fast and to make use of multi-core hardware. Other constituent programs deal with the merging and scaling of large numbers of intensities from randomly oriented snapshot diffraction patterns. The suite uses a generalized representation of a detector to ease the use of more complicated geometries than those familiar in conventional crystallography. The suite is written in C with supporting Perl and shell scripts, and is available as source code under version 3 or later of the GNU General Public License.
407 citations
TL;DR: EDMA as mentioned in this paper is a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules, which locates critical points of the electron density and calculates their principal curvatures.
Abstract: EDMA is a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins. EDMA can also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation of ab initio electron densities obtained in the process of structure solution. A particular feature of EDMA is that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions. EDMA first generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications of EDMA to model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4 or better.
381 citations
TL;DR: PASCal as mentioned in this paper is a web-based tool designed to simplify the determination of principal coefficients of thermal expansion and compressibilities from variable-temperature and variable-pressure lattice parameter data.
Abstract: This article describes a web-based tool (PASCal; principal axis strain calculator; http://pascal.chem.ox.ac.uk) designed to simplify the determination of principal coefficients of thermal expansion and compressibilities from variable-temperature and variable-pressure lattice parameter data. In a series of three case studies, PASCal is used to reanalyse previously published lattice parameter data and show that additional scientific insight is obtainable in each case. First, the two-dimensional metal–organic framework [Cu2(OH)(C8H3O7S)(H2O)]·2H2O is found to exhibit the strongest area negative thermal expansion (NTE) effect yet observed; second, the widely used explosive HMX exhibits much stronger mechanical anisotropy than had previously been anticipated, including uniaxial NTE driven by thermal changes in molecular conformation; and third, the high-pressure form of the mineral malayaite is shown to exhibit a strong negative linear compressibility effect that arises from correlated tilting of SnO6 and SiO4 coordination polyhedra.
363 citations
TL;DR: XDSAPP is a Tcl/Tk-based graphical user interface for the easy and convenient processing of diffraction data sets using XDS that automates the data processing and generates graphical plots of various data set statistics provided by XDS.
Abstract: XDSAPP is a Tcl/Tk-based graphical user interface for the easy and convenient processing of diffraction data sets using XDS. It provides easy access to all XDS functionalities, automates the data processing and generates graphical plots of various data set statistics provided by XDS. By incorporating additional software, further information on certain features of the data set, such as radiation decay during data collection or the presence of pseudo-translational symmetry and/or twinning, can be obtained. Intensity files suitable for CCP4, CNS and SHELX are generated.
242 citations
TL;DR: MossA as mentioned in this paper provides a straightforward approach to the fitting of 57Fe conventional and synchrotron energy-domain Mossbauer spectra, where sites can be defined simply by mouse clicks and hyperfine parameters can be constrained to constant values, within specific ranges, and can be coupled linearly between different subspectra.
Abstract: The program MossA provides a straightforward approach to the fitting of 57Fe conventional and synchrotron energy-domain Mossbauer spectra. Sites can be defined simply by mouse clicks and hyperfine parameters can be constrained to constant values, within specific ranges, and can be coupled linearly between different subspectra. The program includes a full transmission integral fit with Lorentzian line shape (conventional source) or Lorentzian-squared line shape (synchrotron source). The fitting process is graphically displayed in real time while fitting and can be interrupted at any time. Gaussian-shaped quadrupole splitting distributions for analyzing nonmagnetic amorphous materials are included. MossA is designed especially for the rapid and comprehensive analysis of complex Mossbauer spectra, made possible by its native graphical user input.
213 citations
TL;DR: Z-Rietveld as mentioned in this paper is a program suite for Rietvell analysis and the Pawley method; it was developed for analyses of powder diffraction data in the Materials and Life Science Facility of the Japan Proton Accelerator Research Complex.
Abstract: Z-Rietveld is a program suite for Rietveld analysis and the Pawley method; it was developed for analyses of powder diffraction data in the Materials and Life Science Facility of the Japan Proton Accelerator Research Complex. Improvements have been made to the nonlinear least-squares algorithms of Z-Rietveld so that it can deal with singular matrices and intensity non-negativity constraints. Owing to these improvements, Z-Rietveld successfully executes the Pawley method without requiring any constraints on the integrated intensities, even in the case of severely or exactly overlapping peaks. In this paper, details of these improvements are presented and their advantages discussed. A new approach to estimate the number of independent reflections contained in a powder pattern is introduced, and the concept of good reflections proposed by Sivia [J. Appl. Cryst. (2000), 33, 1295–1301] is shown to be explained by the presence of intensity non-negativity constraints, not the intensity linear constraints.
186 citations
TL;DR: A computer program, 3DBVSMAPPER, was developed to generate bond-valence sum maps and bond-Valence energy landscapes with minimal user intervention and has the capacity to process automatically an unlimited number of materials using crystallographic information files as input.
Abstract: A computer program, 3DBVSMAPPER, was developed to generate bond-valence sum maps and bond-valence energy landscapes with minimal user intervention. The program is designed to calculate the spatial distributions of bond-valence values on three-dimensional grids, and to identify infinitely connected isosurfaces in these spatial distributions for a given bond-valence mismatch or energy threshold and extract their volume and surface area characteristics. It is implemented in the Perl scripting language embedded in Accelrys Materials Studio and has the capacity to process automatically an unlimited number of materials using crystallographic information files as input.
TL;DR: The AMPIX cell as mentioned in this paper enables experiments providing greater insight into the complex processes that occur in operating batteries by allowing the electrochemical reactions to be probed at fine reaction intervals with greater consistency with potential for new time-dependent kinetic studies or studies of transient species.
Abstract: This article presents a versatile easy-to-use electrochemical cell suitable for in operando, in situ measurements of battery materials during electrochemical cycling using a variety of X-ray techniques. Argonne's multi-purpose in situ X-ray (AMPIX) cell provides reliable electrochemical cycling over extended periods owing to the uniform stack pressure applied by rigid X-ray windows and the formation of a high-fidelity hermetic seal. The suitability of the AMPIX cell for a broad range of synchrotron-based X-ray scattering and spectroscopic measurements has been demonstrated with studies at eight Advanced Photon Source beamlines to date. Compatible techniques include pair distribution function analysis, high-resolution powder diffraction, small-angle scattering and X-ray absorption spectroscopy. These techniques probe a broad range of electronic, structural and morphological features relevant to battery materials. The AMPIX cell enables experiments providing greater insight into the complex processes that occur in operating batteries by allowing the electrochemical reactions to be probed at fine reaction intervals with greater consistency (within the charge–discharge cycle and between different methodologies) with potential for new time-dependent kinetic studies or studies of transient species. Representative X-ray and electrochemical data to demonstrate the functionality of the AMPIX cell are presented.
TL;DR: The foundations and current features of a widely used graphical user interface for macromolecular crystallography are described.
Abstract: 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.
TL;DR: In this paper, a review of the field is provided, with a viewpoint from materials science, based on the use of highly penetrating hard X-rays from a synchrotron source and the application of tomographic reconstruction algorithms for the analysis of the diffraction data.
Abstract: Three-dimensional X-ray diffraction microscopy is a fast and nondestructive structural characterization technique aimed at studies of the individual crystalline elements (grains or subgrains) within millimetre-sized polycrystalline specimens. It is based on two principles: the use of highly penetrating hard X-rays from a synchrotron source and the application of `tomographic' reconstruction algorithms for the analysis of the diffraction data. In favourable cases, the position, morphology, phase and crystallographic orientation can be derived for up to 1000 elements simultaneously. For each grain its average strain tensor may also be derived, from which the type II stresses can be inferred. Furthermore, the dynamics of the individual elements can be monitored during typical processes such as deformation or annealing. A review of the field is provided, with a viewpoint from materials science.
TL;DR: In this paper, a 40-m-long small-angle neutron scattering (SANS) instrument has been constructed, which utilizes a mechanical velocity selector, pinhole collimation and a high-count-rate (>105-Hz) two-dimensional position-sensitive detector.
Abstract: A series of upgrades have been undertaken at the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory, including the installation of a supercritical hydrogen moderator (T ≃ 20 K), which has boosted the flux of long-wavelength neutrons by over two orders of magnitude. In order to take advantage of the new capabilities, a 40 m-long small-angle neutron scattering (SANS) instrument has been constructed, which utilizes a mechanical velocity selector, pinhole collimation and a high-count-rate (>105 Hz) large-area (1 m2) two-dimensional position-sensitive detector. The incident wavelength (λ), resolution (Δλ/λ), incident collimation and sample-to-detector distance are independently variable under computer control. The detector can be moved up to 45 cm off-axis to increase the overall Q range [<0.001 < Q = (4π/λ)sinθ < 1 A−1, where 2θ is the angle of scatter]. The design and characteristics of this instrument are described, along with examples of scattering data to illustrate the performance.
TL;DR: In this article, the evolution of the crystallographic orientation field in a polycrystalline sample of copper is mapped in three dimensions as tensile strain is applied, and the ability to track intragranular orientation variations is demonstrated on an ∼2'µm length scale with ∼0.1° orientation precision.
Abstract: The evolution of the crystallographic orientation field in a polycrystalline sample of copper is mapped in three dimensions as tensile strain is applied. Using forward-modeling analysis of high-energy X-ray diffraction microscopy data collected at the Advanced Photon Source, the ability to track intragranular orientation variations is demonstrated on an ∼2 µm length scale with ∼0.1° orientation precision. Lattice rotations within grains are tracked between states with ∼1° precision. Detailed analysis is presented for a sample cross section before and after ∼6% strain. The voxel-based (0.625 µm triangular mesh) reconstructed structure is used to calculate kernel-averaged misorientation maps, which exhibit complex patterns. Simulated scattering from the reconstructed orientation field is shown to reproduce complex scattering patterns generated by the defected microstructure. Spatial variation of a goodness-of-fit or confidence metric associated with the optimized orientation field indicates regions of relatively high or low orientational disorder. An alignment procedure is used to match sample cross sections in the different strain states. The data and analysis methods point toward the ability to perform detailed comparisons between polycrystal plasticity computational model predictions and experimental observations of macroscopic volumes of material.
TL;DR: In this article, a first generation synchrotron-class X-ray laboratory microsource coupled with a three-pinhole camera is presented, which allows both small and wide-angle x-ray scattering images to be acquired simultaneously.
Abstract: A first-generation-synchrotron-class X-ray laboratory microsource, coupled to a three-pinhole camera, is presented. It allows (i) small- and wide-angle X-ray scattering images to be acquired simultaneously, and (ii) scanning small- and wide-angle X-ray scattering microscopy to be carried out. As representative applications, the structural complexity of a biological natural material (human bone biopsy) and of a metamaterial (colloidal nanocrystal assembly) are inspected at different length scales, studying the atomic/molecular ordering by (grazing-incidence) wide-angle X-ray scattering and the morphological/structural conformation by (grazing-incidence) small-angle X-ray scattering. In particular, the grazing-incidence measurement geometries are needed for inspecting materials lying on top of surfaces or buried underneath surfaces.
TL;DR: In this article, the structure and morphology of the as-synthesized nanowires were characterized using X-ray diffraction, scanning and transmission electron microscopies, selected area electron diffraction and electron dispersive x-ray spectroscopy.
Abstract: Vertically aligned undoped ZnO and Sb-doped ZnO nanowires have been synthesized on a silicon substrate using the vapor–solid technique, without using a catalyst or predeposited buffer layers. The structure and morphology of the as-synthesized nanowires are characterized using X-ray diffraction, scanning and transmission electron microscopies, selected area electron diffraction, and electron dispersive X-ray spectroscopy. The results showed that the use of Si(111) is a critical factor for the growth of vertically aligned nanowires. This is a result of the lattice match on Si(111), which is more favorable with the ZnO lattice structure because the Si(111) surface is hexagonal and has a smaller lattice constant of 3.840 A. The photoluminescence properties were also investigated at room temperature (300 K). The UV peaks of undoped and Sb-doped ZnO nanowires are located at 3.33 and 3.29 eV, respectively. This redshift of 0.04 eV in the Sb-doped ZnO indicates a reduction of the ZnO band gap caused by the Sb dopant. The temperature-dependent photoluminescence spectra of Sb-doped ZnO nanowires from 10 to 300 K were also examined. This measurement showed that at 10 K several peaks appear, at 3.36, 3.23 and 3.04 eV, which were assigned as acceptor-bound excitons, a donor–acceptor pair and a zinc-vacancy-related peak, respectively. These peaks are shifted with the increase of temperature up to 300 K.
TL;DR: In this article, high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED), and X-ray photoelectron spectroscopy (XPS) images were used to characterize AgInSe2 thin films.
Abstract: Highly stoichiometric AgInSe2 thin films have been prepared on a p-type Si(111) substrate by a sol–gel spin-coating technique. These films were annealed at different temperatures. The as-prepared and annealed films were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), selected area electron diffraction (SAED) and X-ray photoelectron spectroscopy (XPS). The XRD spectra showed that the crystal structure of the AgInSe2 film was that of cubic fluorite chalcopyrite with lattice constants a = 6.102 A and c = 11.69 A. The SEM images depicted the surface morphology as smooth and the spherical particles as uniformly distributed. The average particle size was increased as the annealing temperature increased. Using HRTEM images and SAED patterns for the as-synthesized and annealed thin films, the AgInSe2 film was indexed to a pure polycrystalline chalcopyrite AgInSe2 structure with a lattice spacing of around 0.3 nm. XPS spectra showed that the as-deposited AgInSe2 film was Ag rich, while the AgInSe2 films annealed at 523 and 623 K were In rich.
TL;DR: In this paper, a setup for automated high-throughput measurements of small-angle X-ray scattering (SAXS) from macromolecular solutions on the bending-magnet beamline X33 of EMBL at the storage ring DORIS-III (DESY, Hamburg).
Abstract: A setup is presented for automated high-throughput measurements of small-angle X-ray scattering (SAXS) from macromolecular solutions on the bending-magnet beamline X33 of EMBL at the storage ring DORIS-III (DESY, Hamburg). A new multi-cell compartment allows for rapid switching between in-vacuum and in-air operation, for digital camera assisted control of cell filling and for colour sample illumination. The beamline is equipped with a Pilatus 1 M-W pixel detector for SAXS and a Pilatus 300 k-W for wide-angle scattering (WAXS), and results from the use of the Pilatus detectors for scattering studies are reported. The setup provides a broad resolution range from 100 to 0.36 nm without the necessity of changing the sample-to-detector distance. A new optimized robotic sample changer is installed, permitting rapid and reliable automated sample loading and cell cleaning with a required sample volume of 40 µl. All the devices are fully integrated into the beamline control software system, ensuring fully automated and user-friendly operation (attended, unattended and remote) with a throughput of up to 15 measurements per hour.
TL;DR: Sharma, Huizenga, and Offerman as mentioned in this paper described the procedure for the determination of the grain characteristics for thousands of grains using 3D X-ray diffraction (3DXRD).
Abstract: This second part of the paper on an analysis strategy for data acquired using three-dimensional X-ray diffraction (3DXRD) describes the procedure for the determination of the grain characteristics for thousands of grains. The approach developed here is orders of magnitude faster than those presently available for indexing thousands of grains. Using information obtained from the steps described in Part I [Sharma, Huizenga & Offerman (2012). J. Appl. Cryst. 45, 693–704], the volume, crystallographic orientation, centre-of-mass position and strain state of grains in the sample can be determined. The algorithms dealing with the determination of the orientation, centre-of-mass position and strain state of the grains are divided into two parts. The first deals with indexing, i.e. it assigns diffraction spots to individual grains assuming an unstrained lattice, and the second deals with the refinement of the crystallographic orientation, centre-of-mass position and strain state of the grains using the diffraction spots assigned during indexing. The different approaches to indexing that exist in the literature are presented and compared with the novel approach developed here. Indexing can be run in two modes depending on the number of grains. For large numbers of grains, the approach employs a novel sample `surface' scanning technique, in combination with a reduced number of search orientations, to achieve high robustness and computation efficiency. For small numbers of grains, the approach neglects the position of the diffracting grains in the sample in order to improve the computation efficiency. For unstrained samples, both modes of indexing and the subsequent process of refinement are validated using simulated data for 60 and 3000 grains. In both cases, the centre-of-mass position of the grains was determined with a mean error of 0.7 µm and the orientation was determined with a mean error of 0.0003°. Furthermore, an experiment was `mimicked' by introducing experimental errors into the simulation for 3000 grains. The resulting mean errors in the centre-of-mass position (2.1 µm) and orientation (0.008°) of the grains are higher than those for the ideal simulations, and the errors in an experiment will depend on the `true' experimental errors. The algorithms dealing with strained samples are validated using a simulation for 3000 grains with mimicked experimental errors. The centre-of-mass position, crystallographic orientation, normal strain tensor components and shear strain tensor components of the grains were determined with mean errors of 8 µm, 0.006°, 5.2 × 10−5 and 2.8 × 10−5, respectively. The possibility of obtaining grain-level information for thousands of grains with a high speed of acquisition makes the technique very attractive for in situ studies of thermomechanical processes in polycrystalline materials.
TL;DR: Sharma, Huizenga, and Offerman as discussed by the authors presented a data analysis methodology for the characterization of polycrystalline materials from data acquired using 3D X-ray diffraction (3DXRD).
Abstract: A data-analysis methodology is presented for the characterization of three-dimensional microstructures of polycrystalline materials from data acquired using three-dimensional X-ray diffraction (3DXRD). The method is developed for 3DXRD microscopy using a far-field detector and yields information about the centre-of-mass position, crystallographic orientation, volume and strain state for thousands of grains. This first part deals with pre-processing of the diffraction data for input into the algorithms presented in the second part [Sharma, Huizenga & Offerman (2012). J. Appl. Cryst. 45, 705–718] for determination of the grain characteristics. An algorithm is presented for accurate identification of overlapping diffraction peaks from X-ray diffraction images, which has been an issue limiting the accuracy of experiments of this type. The algorithm works in two stages, namely the identification of overlapping peaks using a seeded watershed algorithm, and then the fitting of the peaks with a pseudo-Voigt shape function to yield an accurate centre-of-mass position and integrated intensity for the peaks. Regions consisting of up to six overlapping peaks can be successfully fitted. Two simulations and an experiment are used to verify the results of the algorithms. An example of the processing of diffraction images acquired in a 3DXRD experiment with a sample consisting of more than 1600 grains is shown. Furthermore, a procedure for the determination of the parameters of the experimental setup (global parameters) without the need for a calibration sample is presented and validated using simulations. This is immensely beneficial for simplifying experiments and the subsequent data analysis.
TL;DR: A web site for indirect transformation of small-angle scattering data is presented and the result of the indirect information is displayed on the screen in the form of a distribution, together with the experimental data and the fit to the data.
Abstract: A web site (http://www.bayesapp.org) for indirect transformation of small-angle scattering data is presented. When experimental data are uploaded to the server, they are processed in a few seconds and the result of the indirect information is displayed on the screen in the form of a distribution, together with the experimental data and the fit to the data. No other user input than the experimental data is necessary, but various options for the analysis may be selected. The results of the analysis can be downloaded from the web site in the form of ASCII files.
TL;DR: MAGNEXT as discussed by the authors is a computer program available from the Bilbao Crystallographic Server that provides symmetry-forced systematic absences or extinction rules of magnetic nonpolarized neutron diffraction.
Abstract: MAGNEXT is a new computer program available from the Bilbao Crystallographic Server (http://www.cryst.ehu.es) that provides symmetry-forced systematic absences or extinction rules of magnetic nonpolarized neutron diffraction. For any chosen Shubnikov magnetic space group, the program lists all systematic absences, and it can also be used to obtain the list of the magnetic space groups compatible with a particular set of observed systematic absences. Absences corresponding to specific ordering modes can be derived by introducing effective symmetry operations associated with them. Although systematic extinctions in neutron diffraction do not possess the strong symmetry-resolving power of those in nonmagnetic crystallography, they can be important for the determination of some magnetic structures. In addition, MAGNEXT provides the symmetry-adapted form of the magnetic structure factor for different types of diffraction vectors, which can then be used to predict additional extinctions caused by some prevailing orientation of the atomic magnetic moments. This program, together with a database containing comprehensive general information on the symmetry operations and the Wyckoff positions of the 1651 magnetic space groups, is the starting point of a new section in the Bilbao Crystallographic Server devoted to magnetic symmetry and its applications.
TL;DR: The Small Angle Scattering ToolBox (SASTBX) as discussed by the authors provides a wide-ranging functionality for the analysis of biological small-angle scattering data, from data reduction to model reconstruction and refinement.
Abstract: Small-angle X-ray and neutron scattering experiments are broadly applied to study biomolecular structure and dynamics. This article presents the Small Angle Scattering ToolBox (SASTBX), which provides a wide-ranging functionality for the analysis of biological small-angle scattering data, from data reduction to model reconstruction and refinement. The SASTBX is an open-source package, which is freely available at http://sastbx.als.lbl.gov.
TL;DR: An automated sample-loading system for BioSAXS beamlines, which combines single-channel disposable-tip pipetting with a vacuum-enclosed temperature-controlled capillary flow cell, and incorporates an easily changeable capillary to reduce the incidence of X-ray window fouling and cross contamination.
Abstract: With the rise in popularity of biological small-angle X-ray scattering (BioSAXS) measurements, synchrotron beamlines are confronted with an ever-increasing number of samples from a wide range of solution conditions. To meet these demands, an increasing number of beamlines worldwide have begun to provide automated liquid-handling systems for sample loading. This article presents an automated sample-loading system for BioSAXS beamlines, which combines single-channel disposable-tip pipetting with a vacuum-enclosed temperature-controlled capillary flow cell. The design incorporates an easily changeable capillary to reduce the incidence of X-ray window fouling and cross contamination. Both the robot-control and the data-processing systems are written in Python. The data-processing code, RAW, has been enhanced with several new features to form a user-friendly BioSAXS pipeline for the robot. The flow cell also supports efficient manual loading and sample recovery. An effective rinse protocol for the sample cell is developed and tested. Fluid dynamics within the sample capillary reveals a vortex ring pattern of circulation that redistributes radiation-damaged material. Radiation damage is most severe in the boundary layer near the capillary surface. At typical flow speeds, capillaries below 2 mm in diameter are beginning to enter the Stokes (creeping flow) regime in which mixing due to oscillation is limited. Analysis within this regime shows that single-pass exposure and multiple-pass exposure of a sample plug are functionally the same with regard to exposed volume when plug motion reversal is slow. The robot was tested on three different beamlines at the Cornell High-Energy Synchrotron Source, with a variety of detectors and beam characteristics, and it has been used successfully in several published studies as well as in two introductory short courses on basic BioSAXS methods.
TL;DR: In this article, an anti-settling sample delivery instrument based on a rotating syringe pump was developed, capable of producing flow rates and liquid pressures necessary for the operation of the injector.
Abstract: Serial femtosecond crystallography (SFX) using X-ray free-electron laser (FEL) sources has the potential to determine the structures of macromolecules beyond the limitation of radiation damage and without the need for crystals of sufficient size for conventional crystallography. In SFX, a liquid microjet is used to inject randomly oriented crystals suspended in their storage solution into the FEL beam. Settling of crystals in the reservoir prior to the injection has been found to complicate the data collection. This article details the development of an anti-settling sample delivery instrument based on a rotating syringe pump, capable of producing flow rates and liquid pressures necessary for the operation of the injector. The device has been used successfully with crystals of different proteins, with crystal sizes smaller than 20 µm. Even after hours of continuous operation, no significant impairment of the experiments due to sample settling was observed. This article describes the working principle of the instrument and sets it in context with regard to the experimental conditions used for SFX. Hit rates for longer measuring periods are compared with and without the instrument operating. Two versions of the instrument have been developed, which both deliver sample at a constant flow rate but which differ in their minimum liquid flow rates and maximum pressures.
TL;DR: In this article, a high-resolution nanodiffraction experiment on a nanocrystalline TiN hard coating was performed to verify the resolution of the nanodeafraction setup and to reveal the local gradients across the blasted TiN coating.
Abstract: The micro- and nanofocus X-ray scattering (MINAXS) beamline of PETRA III is equipped with two consecutively arranged endstations, the last of which is the nanofocus endstation. The first in-beam commissioning of the experimental equipment was successfully performed at the end of 2010, using two-dimensionally confining hard X-ray silicon waveguides with cross sections of 50 nm × 50 µm to 50 nm × 2 µm for nanobeam generation. A full characterization of the waveguide-generated beams was performed, giving values for the beam geometries, the transmission efficiencies of the waveguides and absolute fluxes. Along with these results a detailed description of the setup is presented in this paper. A first high-resolution nanodiffraction experiment on a nanocrystalline TiN hard coating was performed to verify the resolution of the nanodiffraction setup and to reveal the local gradients across the blasted TiN coating. In conclusion, the main concern is the availability of the nanobeam, how it was generated and the fact that a beam out of a two-dimensionally confining waveguide was used for diffraction experiments for the first time.
TL;DR: In this article, Soper et al. compared the effectiveness of the Lorch function with a revised version of this function and found that the two functions produce equivalent results, unless the broadening is allowed to increase with r, in which case the revised Lorch functions is better at suppressing spurious oscillations.
Abstract: When Fourier transforming radiation total scattering data to the pair distribution function it is common to use a `modification' function to help reduce the termination ripples that would otherwise occur as a result of the finite range and counting statistics of the scattering data. One of the most common functions employed was proposed by Lorch [J. Phys. C Solid State Phys. (1969), 2, 229–237]. In a recent article [Soper & Barney (2011). J. Appl. Cryst. 44, 714–726] a revised version of this function was proposed. Here the effectiveness of these two functions at removing spurious structure from Fourier transformed data is compared. It is found that the two functions produce equivalent results, unless the broadening is allowed to increase with r, in which case the revised Lorch function is better at suppressing spurious oscillations. The presence of counting statistics produces a marked increase in the amplitude of the truncation oscillations.
TL;DR: In this paper, the transition from a rod-like to a semicircle-like GISAXS pattern has been simulated and attributed to the contribution of the form factor by changing the length of the line (ripple).
Abstract: Grazing-incidence small-angle X-ray scattering (GISAXS) has been used to structurally characterize model hard and soft gratings of nanotechnological interest. The different gratings exhibit GISAXS patterns with characteristic features that can be associated with their level of order along the direction of periodicity and the length of the lines. Highly ordered gratings, made out of silicon by electron beam lithography, and those nanofabricated on spin-coated polymer films by nanoimprint lithography, exhibit characteristic semicircle-like GISAXS patterns with intensity spots periodically distributed on a semicircle whose radius is related to the incidence angle used. These gratings can be considered as one-dimensional crystalline lattices as provided by computer simulations. Less ordered polymer gratings prepared by the laser-induced periodic surface structuring method exhibit a GISAXS pattern characterized by periodic rod-like scattering maxima whose intensity decreases with increasing horizontal scattering angle. In this case the gratings can be considered as one-dimensional paracrystals. The transition from a rod-like to a semicircle-like GISAXS pattern has been simulated and attributed to the contribution of the form factor by changing the length of the line (ripple). A critical length value for the transition is located at around a few micrometres.