Showing papers in "Journal of Applied Crystallography in 2007"
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations
TL;DR: SUPERFLIP is a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm and has been successfully compiled and tested on a variety of operating systems.
Abstract: SUPERFLIP is a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data. Structure solution from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure. SUPERFLIP is written in Fortran90 and is distributed as a source code and as precompiled binaries. It has been successfully compiled and tested on a variety of operating systems.
3,600 citations
TL;DR: GenX is a versatile program using the differential evolution algorithm for fitting X-ray and neutron reflectivity data, utilizes the Parratt recursion formula for simulating specular reflectivity, and can fit an arbitrary number of data sets simultaneously.
Abstract: GenX is a versatile program using the differential evolution algorithm for fitting X-ray and neutron reflectivity data. It utilizes the Parratt recursion formula for simulating specular reflectivity. The program is easily extensible, allowing users to incorporate their own models into the program. This can be useful for fitting data from other scattering experiments, or for any other minimization problem which has a large number of input parameters and/or contains many local minima, where the differential evolution algorithm is suitable. In addition, GenX manages to fit an arbitrary number of data sets simultaneously. The program is released under the GNU General Public License.
793 citations
TL;DR: Is a suite of computer programs devoted to protein crystal structure determination by X-ray crystallography, which automatically uses the above information to phase protein reflections, and may succeed even with structures with up to 6000 non-H atoms in the asymmetric unit.
Abstract: IL MILIONEIl Milione is the title of the book by Marco Polo, dictated to Rustichello da Pisa in 1298 in the Genova prison where Marco was imprisoned after a naval battle between Genova and Venezia. Il Milione is a travel report: the name suggests the millions of marvels seen during the travel. Most contemporaries thought that they were a million tales. Our program is also a travel report, but in the world of crystallography. is a suite of computer programs devoted to protein crystal structure determination by X-ray crystallography. It may be used in the following key activities. (a) Ab initio phasing, via Patterson or direct methods. The program may succeed even with structures with up to 6000 non-H atoms in the asymmetric unit, provided that atomic resolution is available, and with data at quasi-atomic resolution (1.4–1.5 A). (b) Single or multiple isomorphous replacement, single- or multiple-wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. In the first step the program finds the heavy-atom/anomalous scatterer substructure, then automatically uses the above information to phase protein reflections. Phase extension and refinement are performed by electron density modification techniques. (c) Molecular replacement. The orientation and the location of the protein molecules are found via reciprocal space methods. Phase extension and refinement are performed by electron density modification techniques. All the programs integrated into IL MILIONE are controlled by means of a user-friendly graphical user interface, which is used to input data and to monitor intermediate and final results by means of real-time updated messages, diagrams and histograms.
648 citations
TL;DR: A prototype of an automated data-analysis system for isotropic solution scattering based on the further development of the programs belonging to the package ATSAS 2.1 is reported.
Abstract: Small-angle scattering (SAS) is frequently employed for screening large numbers of samples and for studying these samples under different conditions, including space- and time-resolved analysis. These measurements produce immense amounts of data, especially on modern high-flux and high-brilliance sources (e.g. third-generation synchrotrons). In biological SAS, like high-throughput macromolecular crystallography, large-scale analysis of proteins and macromolecular complexes is also emerging. Automation of data analysis becomes an indispensable prerequisite for adequate evaluation of high-throughput SAS experiments. Here a prototype of an automated data-analysis system for isotropic solution scattering based on the further development of the programs belonging to the package ATSAS 2.1 is reported. This system allows the major analysis tasks starting from the raw data processing and, for monodisperse systems, finishing with a three-dimensional model, to be performed automatically. Convenient web interfaces for the online use of individual ATSAS programs are also provided.
465 citations
TL;DR: The behavior of a number of commonly used pressure media, including nitrogen, argon, 2-propanol, a 4:1 methanol-ethanol mixture, glycerol and various grades of silicone oil, has been examined by measuring the X-ray diffraction maxima from quartz single crystals loaded in a diamond-anvil cell with each of these pressure media in turn.
Abstract: The behavior of a number of commonly used pressure media, including nitrogen, argon, 2-propanol, a 4:1 methanol–ethanol mixture, glycerol and various grades of silicone oil, has been examined by measuring the X-ray diffraction maxima from quartz single crystals loaded in a diamond-anvil cell with each of these pressure media in turn. In all cases, the onset of non-hydrostatic stresses within the medium is detectable as the broadening of the rocking curves of X-ray diffraction peaks from the single crystals. The onset of broadening of the rocking curves of quartz is detected at ∼9.8 GPa in a 4:1 mixture of methanol and ethanol and at ∼4.2 GPa in 2-propanol, essentially at the same pressures as the previously reported hydrostatic limits determined by other techniques. Gigahertz ultrasonic interferometry was also used to detect the onset of the glass transition in 4:1 methanol–ethanol and 16:3:1 methanol–ethanol–water, which were observed to support shear waves above ∼9.2 and ∼10.5 GPa, respectively, at 0.8–1.2 GHz. By contrast, peak broadening is first detected at ∼3 GPa in nitrogen, ∼1.9 GPa in argon, ∼1.4 GPa in glycerol and ∼0.9 GPa in various grades of silicone oil. These pressures, which are significantly lower than hydrostatic limits quoted in the literature, should be considered as the practical maximum limits to the hydrostatic behavior of these pressure media at room temperature.
446 citations
TL;DR: In this article, the molecular mass (MM) of a monodisperse protein solution is calculated from the extrapolated scattering intensity at zero angle I(0), which provides valuable information about the oligomeric state and absence of unspecific aggregation.
Abstract: One of the most important overall parameters, which can be derived from small-angle X-ray scattering (SAXS) experiments on macromolecular solutions is the molecular mass (MM) of the solute. In particular, for a monodisperse protein solution, MM of the solute is calculated from the extrapolated scattering intensity at zero angle I(0). Assessing MM by SAXS provides valuable information about the oligomeric state and absence of unspecific aggregation in solution. The value of MM can either be estimated by comparison with a protein standard with a known MM or by determining the absolute scattering intensity using, e.g., water scattering. In both cases, knowledge about the solute concentration and about the partial specific volume of the protein is required. By measuring 13 well characterized globular proteins with MMs ranging from 13.7 to 669 kDa we analyze the sources of possible systematic deviations and assess the accuracy of MM determination using SAXS. The data indicate that all these proteins have approximately the same `effective' value of the partial specific volume of about 0.7425 cm3 g−1. It is shown that both inter-protein and water calibration can be used for molecular mass determination by SAXS and in most cases the errors do not exceed 10%.
366 citations
TL;DR: A computer program has been written to reconstruct the parent grains from EBSD data of phase transition materials to help improve the quality of EBSD-based materials used in electronics engineering.
Abstract: A computer program called ARPGE written in Python uses the theoretical results generated by the computer program GenOVa to automatically reconstruct the parent grains from electron backscatter diffraction data obtained on phase transition materials with or without residual parent phase. The misorientations between daughter grains are identified with operators, the daughter grains are identified with indexed variants, the orientations of the parent grains are determined, and some statistics on the variants and operators are established. Some examples with martensitic transformations in iron and titanium alloys were treated. Variant selection phenomena were revealed.
269 citations
TL;DR: In this article, a major upgrade of the small-angle X-ray scattering beamline X33 was performed to improve the beamline stability and data quality, to shorten the measurement time and to ensure user-friendly operation.
Abstract: The small-angle X-ray scattering beamline X33 of the European Molecular Biology Laboratory (EMBL) at the DORIS III storage ring [Deutsches Elektronen Synchrotron (DESY) Hamburg] was used for more than two decades to study the structure of non-crystalline biological systems. During recent years the beamline's scope has changed and is now predominantly used to analyze solutions of biological macromolecules. Owing to renewed interest in solution scattering studies from the biological community, the workload on the beamline has steadily increased. A major upgrade of X33 was performed to improve the beamline stability and data quality, to shorten the measurement time and to ensure user-friendly operation. The upgrade involved all major components of the beamline, including the optical system (monochromator, mirror, slits, beam monitors), electronics, control and acquisition software, X-ray detector system and the sample environment. The upgrade improved the brilliance by a factor of about three and the measuring time was reduced by a factor of seven. The knowledge and experience gained during the implementation of the upgrades to X33, may aid the design process for the BioSAXS beamline to be constructed for the PETRA-3 facility at DESY.
248 citations
TL;DR: In this paper, the application of a large area (41 × 41 cm, 2048 × 2048 or 1024 × 1024 pixel) high-sensitivity detector based on an amorphous silicon array system to the collection of high-energy X-ray scattering data for quantitative pair distribution function analysis is evaluated and discussed.
Abstract: The application of a large-area (41 × 41 cm, 2048 × 2048 or 1024 × 1024 pixel) high-sensitivity (detective quantum efficiency > 65%) fast-readout (up to 7.5 or 30 Hz) flat-panel detector based on an amorphous silicon array system to the collection of high-energy X-ray scattering data for quantitative pair distribution function (PDF) analysis is evaluated and discussed. Data were collected over a range of exposure times (0.13 s–7 min) for benchmark PDF samples: crystalline nickel metal and amorphous silica (SiO2). The high real-space resolution of the resultant PDFs (with Qmax up to ∼40 A−1) and the high quality of fits to data [RNi(0.13s) = 10.5%, RNi(1.3s) = 6.3%] obtained in short measurement times indicate that this detector is well suited to studies of materials disorder. Further applications of the detector to locate weakly scattering H2 molecules within the porous Prussian blue system, {\rm Mn}^{\rm II}_{\,3}[CoIII(CN)6]2·xH2, and to follow the in situ reduction of PtIVO2 to Pt0 at 30 Hz, confirm the high sensitivity of the detector and demonstrate a new potential for fast time-resolved studies.
202 citations
TL;DR: In this article, the authors used the Bravais-Friedel, Donnay-Harker model to predict crystal morphologies from data stored in files in the CIF format.
Abstract: Crystal morphologies are predicted from data stored in files in the CIF format (crystallographic information file standard of the International Union of Crystallography) on the basis of the Bravais–Friedel, Donnay–Harker model. Several simple improvements to the calculation are introduced with WinXMorph, version 1.4.9, in conjunction with illustrations of the morphologies of quartz, sucrose, lactose, pyrite and lysozyme. The morphologies of the recently discovered pentamorphs of 1,8-dihydroxyanthraquinone are predicted. WinXMorph is available free-of-charge for educational use.
TL;DR: The use of ‘parametric Rietveld refinement’ to extract information from large numbers of powder diffraction patterns using a single evolving structural model is described.
Abstract: In this paper the method of parametric Rietveld refinement is described, in which an ensemble of diffraction data collected as a function of time, temperature, pressure or any other variable are fitted to a single evolving structural model. Parametric refinement offers a number of potential benefits over independent or sequential analysis. It can lead to higher precision of refined parameters, offers the possibility of applying physically realistic models during data analysis, allows the refinement of `non-crystallographic' quantities such as temperature or rate constants directly from diffraction data, and can help avoid false minima.
TL;DR: A review of diffraction techniques for determining residual stress by diffraction can be found in this article, where the best method will vary depending on the particular application under consideration and situations for which each method are appropriate.
Abstract: The determination of residual stress by diffraction depends on the correct measurement of the strain-free lattice spacing d_{hkl}^0, or alternatively the enforcement of some assumption about the state of strain or stress within the body. It often represents the largest uncertainty in residual stress measurements since there are many ways in which the strain-free lattice spacing can vary in ways that are unrelated to stress. Since reducing this uncertainty is critical to improving the reliability of stress measurements, this aspect needs to be addressed, but it is often inadequately considered by experimenters. Many different practical strategies for the determining of d_{hkl}^0 or dref have been developed, some well known, others less so. These are brought together here and are critically reviewed. In practice, the best method will vary depending on the particular application under consideration. Consequently, situations for which each method are appropriate are identified with reference to practical examples.
TL;DR: In this article, the contribution of density fluctuations is considered as a function of the contrast lengths and of the isothermal compressibility of the sample, and a new result is given for numerical evaluations of the different terms of the inherent sample background.
Abstract: Small-angle neutron scattering has been successfully used since the 1970s. As a general rule, methods to extract the useful signal from that received by the detector are well known and give good results. At the Laboratoire Leon Brillouin, for example, these methods have been employed for a long time. However, the data reduction software has been changed for the following reasons. Problems are encountered if the container of the sample gives a spurious signal or if the scattering angle is so large that its cosine cannot be approximated by 1. In the present paper, generalizations of formulas are made in order to account for these difficulties. The decrease of scattered intensity delivered by an incoherent sample that is often observed at large angles is shown to be only due to a geometrical effect. The consequent modifications of the relations used for the normalization of cells of position-sensitive detectors and for the absolute calibration are given. As for the inherent background of the sample, the contribution of density fluctuations is usually neglected. This contribution is formally given as a function of the contrast lengths and of the isothermal compressibility of the sample. This new result allows numerical evaluations of the different terms of the inherent sample background. Practical examples are given. Finally, several methods, developed at the Laboratoire Leon Brillouin, are given to determine the background properly. They are based on systematic measurements of transmissions and background levels of suitably prepared blank samples.
TL;DR: A new version of MCE is described in this paper, which supports atomposition generation based on space groups and can display more unit cells around the basic unit cell, and display settings have been improved to allow the colors of the background, atoms and maps to be changed.
Abstract: A new version of MCE is described. This new version supports atom-position generation based on space groups and can display more unit cells around the basic unit cell. The display settings have been improved to allow the colors of the background, atoms and maps to be changed.
TL;DR: The beamline 4-2 at the Stanford Synchrotron Radiation Laboratory is a small-angle X-ray scattering/diffraction facility dedicated to structural studies on mostly non-crystalline biological systems.
Abstract: Beamline 4-2 at the Stanford Synchrotron Radiation Laboratory is a small-angle X-ray scattering/diffraction facility dedicated to structural studies on mostly noncrystalline biological systems. The instrument consists of a pinhole camera, which covers the magnitude of the scattering vector Q in the range 0.004–1.3 A−1 [Q = (4π/λ)sin θ, where θ and λ are one half of the scattering angle and the X-ray wavelength, respectively], and a Bonse–Hart geometry ultra-small-angle X-ray scattering setup for the Q range an order of magnitude smaller. The pinhole camera allows quick automated distance and detector selection among any combination of five distances and three position-sensitive detectors. The double-crystal monochromator can have either Si 111 crystals or a pair of synthetic multilayer diffractive elements for higher flux applications. We have adopted a suite of software originally developed for macromolecular crystallography for integrated beamline control as well as static and slow time-resolved small-angle scattering data collection. This article outlines recent technological developments and specialized instrumentation for conducting noncrystalline scattering experiments in structural biology at improved time and spatial resolutions.
TL;DR: InvariomTool as mentioned in this paper is a preprocessor for the XD package that allows the analysis of a structure in terms of the local atomic bonding environment in order to assign Hansen-Coppens pseudoatoms that are transferable from one molecule to another.
Abstract: The program InvariomTool can be used to obtain high-quality X-ray structures of organic molecules by automating both invariom modelling and the modelling process employed in experimental charge density studies. InvariomTool is a preprocessor program for the XD package [Koritsanszky et al. (2003), Technical Report, Freie Universitat Berlin] and allows the analysis of a structure in terms of the local atomic bonding environment in order to assign Hansen–Coppens pseudoatoms that are transferable from one molecule to another (invarioms). It relies on a database of invariom entries, each containing the invariom name, local atomic site symmetry, coordinate system, model-compound name and theoretically predicted multipole population parameters. The information on chemical equivalence and local atomic site symmetry determines which multipole parameters are to be refined in the least-squares procedure of an experimental charge density study. InvariomTool allows the user to generate input files either for invariom refinement, where parameters are fixed and taken from the database, or for an experimental refinement of multipole parameters.
TL;DR: The computer program DRAWxtl produces crystal structure drawings in the form of an interactive screen representation, as well as VRML files for use on web pages and in classroom teaching, and creates input files for the popular Persistence of Vision Raytracer rendering program for publication-quality graphics.
Abstract: The computer program DRAWxtl produces crystal structure drawings in the form of an interactive screen representation, as well as VRML files for use on web pages and in classroom teaching, and creates input files for the popular Persistence of Vision Raytracer (POV-Ray) rendering program for publication-quality graphics, including generation of stereo pairs. DRAWxtl output produces the standard kinds of graphical representations: spheres, ellipsoids, bonds and polyhedra of any complexity. In addition, it can draw arrows to represent magnetic moments, show capped cones to indicate the location of lone-pair electrons and display Fourier contours in three dimensions. A unique feature of this program is the ability to plot incommensurately modulated and composite structures. This open-source program can be used with operating systems as diverse as Windows (9X, NT, 2000 and XP), Mac OS X, Linux and most other varieties of Unix.
TL;DR: CLEARER as mentioned in this paper is a computer program that aids the detailed analysis of polycrystalline fiber diffraction patterns, which can provide structural information about polymers and biopolymers that is unobtainable using other methods.
Abstract: Fibre diffraction can provide structural information about polymers and biopolymers that is unobtainable using other methods. This method has been used to elucidate the structures of many polymers, biopolymers and protein assemblies. Extracting structural information from fibre diffraction patterns is a major challenge. A computer program called CLEARER has been developed that aids the detailed analysis of polycrystalline fibre diffraction patterns. It offers an easy-to-use interface that enables diffraction data processing, analysis and simulation of diffraction patterns. It is likely to be applicable to structural determination for a wide range of polymeric fibrous materials. CLEARER simplifies and speeds up the data analysis process and helps to utilize all of the structural information present in the analysed X-ray and electron diffraction patterns.
TL;DR: In this paper, a pinhole small-angle neutron scattering spectrometer (SANS-J-II) was reconstructed as a focusing and polarized neutron small angle scattering (USAS) detector.
Abstract: SANS-J (a pinhole small-angle neutron scattering spectrometer at research reactor JRR3, Tokai, Japan) was reconstructed as a focusing and polarized neutron small-angle scattering spectrometer (SANS-J-II). By employing focusing lenses of a biconcave MgF2 crystal or of a sextupole permanent magnet and a high-resolution photomultiplier, the minimum accessible magnitude of the scattering vector qmin was improved from 3 × 10−3 A−1 to an ultra-small-angle scattering (USAS) of 3 × 10−4 A−1. Compared with a Bonse–Hart double-crystal method, the advantages of focusing USAS are the efficient detection of anisotropic USAS with an area detector, an improvement in q resolution Δq/q at conventional magnitudes of the scattering vector q ~ 10−3 A−1 and a gain in neutron flux in the conventional q region of q ~ 10−3 A−1.
TL;DR: In this paper, an extension of the dislocation-induced broadening model, valid for any lattice symmetry, is proposed, where dislocation effects are modelled through the description of a dislocation contrast factor in terms of a crystallographic invariant whose terms can be either calculated when the material constants and slip systems are known and refined on the experimental data for an effective estimation of dislocation effect.
Abstract: Owing to the lack of proper models, mainly for the strain broadening component due to dislocations, full exploitation of whole powder pattern modelling for the microstructural analysis of materials has been limited so far to high-symmetry lattices. An extension of the dislocation-induced broadening model, valid for any lattice symmetry, is proposed here. Dislocation effects are modelled through the description of the dislocation contrast factor in terms of a crystallographic invariant whose terms can be either calculated when the material constants and slip systems are known (allowing a dislocation density to be refined) or refined on the experimental data for an effective estimation of dislocation effects.
TL;DR: In this article, an effective reciprocal space mapping scheme has been developed to find and index thin-film reflections which are related to previously known molecular structures, by method of elimination, thinfilm reflections due to novel thinfilm phases can be identified.
Abstract: Thin films of small molecules relevant to organic electronics applications often show a confusing degree of polymorphism. An effective reciprocal-space mapping scheme has been developed in order to find and index thin-film reflections which are related to previously known molecular structures. By method of elimination, thin-film reflections due to novel thin-film phases can thus be identified.
TL;DR: In this article, the grain size distributions of chalcopyrite-type thin-film solar absorbers in completed solar cells were studied in cross section by means of electron-backscatter diffraction.
Abstract: CuInSe2, CuGaSe2, Cu(In,Ga)Se2 and CuInS2 thin-film solar absorbers in completed solar cells were studied in cross section by means of electron-backscatter diffraction. From the data acquired, grain-size distributions were extracted, and also the most frequent grain boundaries were determined. The grain-size distributions of all chalcopyrite-type thin films studied can be described well by lognormal distribution functions. The most frequent grain-boundary types in these thin films are 60°−〈221〉tet and 71°−〈110〉tet (near) Σ3 twin boundaries. These results can be related directly to the importance of {112}tet planes during the topotactical growth of chalcopyrite-type thin films. Based on energetic considerations, it is assumed that the most frequent twin boundaries exhibit a 180°−〈221〉tet constellation.
TL;DR: In this article, a combination of microbeam synchrotron X-ray texture analysis with thin sections of osteonal bone is used to measure the three-dimensional distribution of the c-axis orientation of the mineral apatite in bone with positional resolution of 1'µm.
Abstract: Texture analysis with microbeam scanning diffraction enables the local mapping of three-dimensional crystallite orientation in heterogeneous natural and synthetic materials. Cortical (compact) bone is an example of a hierarchically structured biocomposite, which is built mainly of cylindrical osteons, having a lamellar texture at the micrometre level. In this work, a combination of microbeam synchrotron X-ray texture analysis with thin sections of osteonal bone is used to measure the three-dimensional distribution of the c-axis orientation of the mineral apatite in bone with positional resolution of 1 µm. The data reduction procedure needed to go from the stereographic projection of X-ray intensity to the determination of the local orientation of mineralized collagen fibrils is described. The procedure can be applied to other mineralized tissues (such as trabecular bone and chitin) with micrometre scale and biologically controlled fibrillar texture.
TL;DR: In this paper, a model-independent determination of element-specific partial structures at buried interfaces using the phase-dependent behavior of resonant anomalous X-ray reflectivity (RAXR) data is described.
Abstract: A formalism for model-independent determination of element-specific partial structures at buried interfaces using the phase-dependent behavior of resonant anomalous X-ray reflectivity (RAXR) data is described. Each RAXR spectrum (i.e. reflectivity versus energy at a fixed momentum transfer near the absorption edge of interest) is uniquely constrained by the amplitude and phase of the resonant partial structure factor with pre-determined non-resonant total structure factor and anomalous dispersion corrections of the resonant species. The element-specific partial density distribution is then imaged by discrete Fourier synthesis with the partial structure factor. The utility of this approach is demonstrated in the comparison of Rb+ and Sr2+ distributions at muscovite (001)–aqueous solution interfaces derived by model-independent and model-dependent approaches. This imaging method is useful for rapid determination of complex buried interfacial structures where element-specific atomic distributions are poorly constrained by conventional X-ray reflectivity analysis.
TL;DR: In this paper, the authors describe the parametrization of the raw data and introduce the programs developed for this purpose, including all corrections that can be made without any specific knowledge of the sample, e.g. detector dark-image correction, division by a flat-field and intensity normalization.
Abstract: At the beamlines ID01 and ID02 of the European Synchrotron Radiation Facility in Grenoble, France, position-sensitive detectors for time-resolved small- and wide-angle X-ray scattering experiments are in use. The applied data reduction method has never been described comprehensively. This article outlines the parametrization of the raw data and introduces the programs developed for this purpose. Data reduction in the sense of this article means all steps between detector readout and normalization to absolute scattering intensities. This includes all corrections that can be made without any specific knowledge of the sample, e.g. detector dark-image correction, division by a flat-field and intensity normalization. Processed data are either two- or one-dimensional. Optionally, statistical errors can be propagated through the calculations.
TL;DR: ASTRA2.0 as mentioned in this paper is a program package for single-crystal structure research using different experimental conditions and radiation of different types (X-rays, neutrons and electrons).
Abstract: ASTRA2.0 is a program package for single-crystal structure research using different experimental conditions and radiation of different types (X-rays, neutrons and electrons). The package includes programs for data collection optimization, data reduction, structural parameter refinement and electron density plotting. The expression that is responsible for minimization of the difference between reduced measurements is included in the goal function of the refinement program. The refinement program is based on an adaptive nonlinear least-squares method. The crystal structure is described by a detailed model for electron density analysis. ASTRA uses a multipole model up to eighth order for the aspherical electron density description, an anharmonic model up to sixth order for the description of atom displacement and a model of mixed atomic positions for the description of atomic replacement. Refinement of the structural parameters using data of precession electron diffraction and the Bloch-wave method to account for multiwave scattering is realized. Tools for refinement automation are included in ASTRA.
TL;DR: In this paper, a grating made of lines having a height of 55 nm and a period of 450 nm has been characterized by grazing-incidence small-angle X-ray scattering (GISAXS).
Abstract: In this work a grating made of lines having a height of 55 nm and a period of 450 nm has been characterized by grazing-incidence small-angle X-ray scattering (GISAXS). The GISAXS patterns are characterized by a series of spots corresponding to the intersection of the Ewald sphere with the grating truncation rods (GTRs). When the grating lines are almost parallel to the direct beam, the location of these spots is very sensitive to any change in the azimuthal angle. The precise location of the intersection of the GTRs with the Ewald sphere can be calculated for any azimuthal angle. From this analysis we can estimate the statistical coverage of the grating, its period and the width of the lines. In addition, the anisotropy of the width of the spots in the qz direction is interpreted in terms of wavelength spread and angular divergence of the incident beam.
TL;DR: In this paper, the authors used a micro-spectro-photometer at the European Synchrotron Radiation Facility, Grenoble, France, to measure the signal decay of fluorescent samples.
Abstract: Synchrotrons are now producing thousands of macromolecular structures each year. The need for complementary techniques available on site has progressively emerged, either to assess the relevance of the structure of a protein or to monitor changes that may occur during X-ray diffraction data collection. Microspectrophotometers in the UV–visible absorbance or fluorescence mode have evolved over the past few decades to become the instruments of choice to perform such tests. Described here are recent improvements to the microspectrophotometer of the so-called Cryobench laboratory located at the European Synchrotron Radiation Facility, Grenoble, France. Optical and mechanical properties have been enhanced so as to record better spectra on smaller samples. A device has been implemented to measure the signal decay of fluorescent samples, either in the crystalline or in the solution state. Recording of the fluorescence lifetime in addition to the steady-state fluorescence emission spectrum allows precise monitoring of the fluorescent sample under study. The device consists of an adaptation of a commercially available time-correlated single-photon-counting (TCSPC) system. A method to record and analyze series of TCSPC histograms, e.g. collected as a function of temperature, is described. To validate the instruments, fluorescence lifetimes of fluorescent small molecules or proteins in the crystalline or solution state, at room and cryo temperatures, have been measured. Lifetimes of a number of fluorescent proteins of the GFP family were generally found to be shorter in crystals than in solution, and slightly longer at cryo temperatures than at ambient temperature. The possibility of performing fluorescence lifetime measurements on crystals at synchrotron facilities widens the variety of spectroscopic techniques complementing X-ray diffraction on macromolecular crystallography beamlines.