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Journal of Applied Crystallography

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https://www.readbyqxmd.com/read/29217993/hierarchical-clustering-for-multiple-crystal-macromolecular-crystallography-experiments-the-cccluster-program
#1
Gianluca Santoni, Ulrich Zander, Christoph Mueller-Dieckmann, Gordon Leonard, Alexander Popov
This article describes ccCluster, a software providing an intuitive graphical user interface (GUI) and multiple functions to perform hierarchical cluster analysis on multiple crystallographic datasets. The program makes it easier for users to choose, in the case of multi-crystal data collection, those datasets that will be merged together to give good final statistics. It provides a simple GUI to analyse the dendrogram and various options for automated clustering and data merging.
December 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29217992/the-modular-small-angle-x-ray-scattering-data-correction-sequence
#2
B R Pauw, A J Smith, T Snow, N J Terrill, A F Thünemann
Data correction is probably the least favourite activity amongst users experimenting with small-angle X-ray scattering: if it is not done sufficiently well, this may become evident only during the data analysis stage, necessitating the repetition of the data corrections from scratch. A recommended comprehensive sequence of elementary data correction steps is presented here to alleviate the difficulties associated with data correction, both in the laboratory and at the synchrotron. When applied in the proposed order to the raw signals, the resulting absolute scattering cross section will provide a high degree of accuracy for a very wide range of samples, with its values accompanied by uncertainty estimates...
December 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29217991/variant-selection-in-surface-martensite
#3
Annick P Baur, Cyril Cayron, Roland E Logé
A significant variant selection is reported in isothermal martensite formed on the surface of an Fe-30% Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic-body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}γ habit plane and the accommodation mechanism by twin-related variant pairing...
December 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29217990/the-electrostatic-potential-of-dynamic-charge-densities
#4
Christian B Hübschle, Sander van Smaalen
A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method...
December 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29217989/bayesian-inference-of-metal-oxide-ultrathin-film-structure-based-on-crystal-truncation-rod-measurements
#5
Masato Anada, Yoshinori Nakanishi-Ohno, Masato Okada, Tsuyoshi Kimura, Yusuke Wakabayashi
Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories...
December 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29021738/erratum-expanding-lorentz-and-spectrum-corrections-to-large-volumes-of-reciprocal-space-for-single-crystal-time-of-flight-neutron-diffraction-corrigendum
#6
Tara M Michels-Clark, Andrei T Savici, Vickie E Lynch, Xiaoping Wang, Michal Chodkiewicz, Thomas Weber, Hans-Beat Bürgi, Christina M Hoffmann
[This corrects the article DOI: 10.1107/S1600576716001369.].
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29021737/bioxtas-raw-improvements-to-a-free-open-source-program-for-small-angle-x-ray-scattering-data-reduction-and-analysis
#7
Jesse Bennett Hopkins, Richard E Gillilan, Soren Skou
BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes...
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29021736/nanocrystallography-measurements-of-early-stage-synthetic-malaria-pigment
#8
Ruben A Dilanian, Victor Streltsov, Hannah D Coughlan, Harry M Quiney, Andrew V Martin, Nectarios Klonis, Con Dogovski, Sébastien Boutet, Marc Messerschmidt, Garth J Williams, Sophie Williams, Nicholas W Phillips, Keith A Nugent, Leann Tilley, Brian Abbey
The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage...
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29021735/quantifying-adsorption-induced-deformation-of-nanoporous-materials-on-different-length-scales
#9
Roland Morak, Stephan Braxmeier, Lukas Ludescher, Florian Putz, Sebastian Busch, Nicola Hüsing, Gudrung Reichenauer, Oskar Paris
A new in situ setup combining small-angle neutron scattering (SANS) and dilatometry was used to measure water-adsorption-induced deformation of a monolithic silica sample with hierarchical porosity. The sample exhibits a disordered framework consisting of macropores and struts containing two-dimensional hexagonally ordered cylindrical mesopores. The use of an H2O/D2O water mixture with zero scattering length density as an adsorptive allows a quantitative determination of the pore lattice strain from the shift of the corresponding diffraction peak...
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29021734/calibrating-sans-data-for-instrument-geometry-and-pixel-sensitivity-effects-access-to-an-extended-q-range
#10
Lukas Karge, Ralph Gilles, Sebastian Busch
An improved data-reduction procedure is proposed and demonstrated for small-angle neutron scattering (SANS) measurements. Its main feature is the correction of geometry- and wavelength-dependent intensity variations on the detector in a separate step from the different pixel sensitivities: the geometric and wavelength effects can be corrected analytically, while pixel sensitivities have to be calibrated to a reference measurement. The geometric effects are treated for position-sensitive (3)He proportional counter tubes, where they are anisotropic owing to the cylindrical geometry of the gas tubes...
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29021733/berkeley-screen-a-set-of-96-solutions-for-general-macromolecular-crystallization
#11
Jose H Pereira, Ryan P McAndrew, Giovani P Tomaleri, Paul D Adams
Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing...
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/29021732/nanoparticle-size-distribution-quantification-results-of-a-small-angle-x-ray-scattering-inter-laboratory-comparison
#12
Brian R Pauw, Claudia Kästner, Andreas F Thünemann
This paper presents the first worldwide inter-laboratory comparison of small-angle X-ray scattering (SAXS) for nanoparticle sizing. The measurands in this comparison are the mean particle radius, the width of the size distribution and the particle concentration. The investigated sample consists of dispersed silver nanoparticles, surrounded by a stabilizing polymeric shell of poly(acrylic acid). The silver cores dominate the X-ray scattering pattern, leading to the determination of their radius size distribution using (i) the generalized indirect Fourier transformation method, (ii) classical model fitting using SASfit and (iii) a Monte Carlo fitting approach using McSAS...
October 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808439/saxs4coll-an-integrated-software-tool-for-analysing-fibrous-collagen-based-tissues
#13
Ahmed Abass, James S Bell, Martin T Spang, Sally Hayes, Keith M Meek, Craig Boote
This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808438/atsas-2-8-a-comprehensive-data-analysis-suite-for-small-angle-scattering-from-macromolecular-solutions
#14
D Franke, M V Petoukhov, P V Konarev, A Panjkovich, A Tuukkanen, H D T Mertens, A G Kikhney, N R Hajizadeh, J M Franklin, C M Jeffries, D I Svergun
ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808437/how-to-assign-a-3%C3%A2-%C3%A2-1-dimensional-superspace-group-to-an-incommensurately-modulated-biological-macromolecular-crystal
#15
Jason Porta, Jeff Lovelace, Gloria E O Borgstahl
Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808436/ewald-an-extended-wide-angle-laue-diffractometer-for-the-second-target-station-of-the-spallation-neutron-source
#16
Leighton Coates, Lee Robertson
Visualizing hydrogen atoms in biological materials is one of the biggest remaining challenges in biophysical analysis. While X-ray techniques have unrivaled capacity for high-throughput structure determination, neutron diffraction is uniquely sensitive to hydrogen atom positions in crystals of biological materials and can provide a more complete picture of the atomic and electronic structures of biological macromolecules. This information can be essential in providing predictive understanding and engineering control of key biological processes, for example, in catalysis, ligand binding and light harvesting, and to guide bioengineering of enzymes and drug design...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808435/double-cone-of-eigendirections-in-optically-active-ethylenediammonium-selenate-crystals
#17
Alexander T Martin, Shane M Nichols, Sichao Li, Melissa Tan, Bart Kahr
Circular birefringence (CB) is generally responsible for only a small perturbation to the state of light polarization in crystals that also exhibit linear birefringence (LB). As such, the magnetoelectric tensor of gyration, which gives rise to CB and optical activity, is less well determined than the electric permittivity tensor in optical models of the Mueller matrix. To visualize the effect of the magnetoelectric tensor on polarimetric measurements, reported here are experimental mappings of the Mueller matrix and of the CB in a new chiral crystal with accidental null LB at an accessible optical frequency...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808434/continuous-diffraction-of-molecules-and-disordered-molecular-crystals
#18
Henry N Chapman, Oleksandr M Yefanov, Kartik Ayyer, Thomas A White, Anton Barty, Andrew Morgan, Valerio Mariani, Dominik Oberthuer, Kanupriya Pande
The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808433/felix-an-algorithm-for-indexing-multiple-crystallites-in-x-ray-free-electron-laser-snapshot-diffraction-images
#19
Kenneth R Beyerlein, Thomas A White, Oleksandr Yefanov, Cornelius Gati, Ivan G Kazantsev, Nicolai Fog-Gade Nielsen, Peter M Larsen, Henry N Chapman, Søren Schmidt
A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues-Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808432/grazing-incidence-small-angle-neutron-scattering-from-structures-below-an-interface
#20
Shirin Nouhi, Maja S Hellsing, Vassilios Kapaklis, Adrian R Rennie
Changes of scattering are observed as the grazing angle of incidence of an incoming beam increases and probes different depths in samples. A model has been developed to describe the observed intensity in grazing-incidence small-angle neutron scattering (GISANS) experiments. This includes the significant effects of instrument resolution, the sample transmission, which depends on both absorption and scattering, and the sample structure. The calculations are tested with self-organized structures of two colloidal samples with different size particles that were measured on two different instruments...
August 1, 2017: Journal of Applied Crystallography
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