scholarly journals Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF

2013 ◽  
Vol 46 (3) ◽  
pp. 804-810 ◽  
Author(s):  
Stéphanie Monaco ◽  
Elspeth Gordon ◽  
Matthew W. Bowler ◽  
Solange Delagenière ◽  
Matias Guijarro ◽  
...  
Keyword(s):  
Diffraction Data ◽  
High Speed ◽  
Automatic Processing ◽  
European Synchrotron Radiation Facility ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Computing Environment ◽  
X Ray ◽  
Standard Integration ◽  
Intuitive Manner

The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.

scholarly journals HiSPoD: a program for high-speed polychromatic X-ray diffraction experiments and data analysis on polycrystalline samples

2016 ◽  
Vol 23 (4) ◽  
pp. 1046-1053 ◽  
Author(s):  
Tao Sun ◽  
Kamel Fezzaa
Keyword(s):  
Diffraction Data ◽  
High Speed ◽  
Short Pulse ◽  
Frame Rate ◽  
Short Exposure ◽  
X Rays ◽  
X Ray Diffraction ◽  
Short Exposure Time ◽  
X Ray ◽  
Structure Information

A high-speed X-ray diffraction technique was recently developed at the 32-ID-B beamline of the Advanced Photon Source for studying highly dynamic, yet non-repeatable and irreversible, materials processes. In experiments, the microstructure evolution in a single material event is probed by recording a series of diffraction patterns with extremely short exposure time and high frame rate. Owing to the limited flux in a short pulse and the polychromatic nature of the incident X-rays, analysis of the diffraction data is challenging. Here,HiSPoD, a stand-alone Matlab-based software for analyzing the polychromatic X-ray diffraction data from polycrystalline samples, is described. WithHiSPoD, researchers are able to perform diffraction peak indexing, extraction of one-dimensional intensity profiles by integrating a two-dimensional diffraction pattern, and, more importantly, quantitative numerical simulations to obtain precise sample structure information.

scholarly journals A history of experimental phasing in macromolecular crystallography

2016 ◽  
Vol 72 (3) ◽  
pp. 293-295 ◽  
Author(s):  
Neil Isaacs
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Diffraction Data ◽  
Fourier Transforms ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Crystal Lattices ◽  
X Ray ◽  
Experimental Phasing ◽  
History Of

It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some decades before experimental phasing methods were developed. Many scientists contributed to this development and this paper presents the author's own perspective on this history. There will be other perspectives, so what follows isahistory, rather thanthehistory, of experimental phasing.

scholarly journals Visualisation of membrane protein crystals using X-ray imaging

2014 ◽  
Vol 70 (a1) ◽  
pp. C351-C351
Author(s):  
Anna Warren ◽  
Wes Armour ◽  
Danny Axford ◽  
Mark Basham ◽  
Thomas Connolley ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Cubic Phase ◽  
Informed Decision Making ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Shape Estimation ◽  
X Ray ◽  
Raster Scanning ◽  
X Ray Imaging

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallise on much smaller scales and are frequently mounted in opaque or highly refractive materials.[1,2] It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this poster the use of X-ray microradiography and microtomography is reported as a tool for crystal visualisation, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals, and crystals mounted in opaque materials such as lipidic cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to a diffraction grid scan. However, for sample location and shape estimation alone, just a few radiographic projections may be required; hence reducing the dose the crystals will be exposed to prior to the diffraction data collection.[3]

A system for collection and on-line integration of X-ray diffraction data from a multiwire area detector

1987 ◽  
Vol 20 (3) ◽  
pp. 235-242 ◽  
Author(s):  
M. Blum ◽  
P. Metcalf ◽  
S. C. Harrison ◽  
D. C. Wiley
Keyword(s):  
Diffraction Data ◽  
High Speed ◽  
X Ray Diffraction ◽  
Quality Of Data ◽  
X Ray ◽  
Camera Control ◽  
Area Detector ◽  
C Programming ◽  
On Line ◽  
Integrated Intensities

A system for collecting and measuring X-ray diffraction data from protein crystals has been developed for a multiwire area detector. Computer programs run concurrently on two microcomputers, which collect and reduce detector data to integrated intensities. The self-contained system consists of an X-ray area detector, a rotation/oscillation camera, and two microcomputers connected by a high-speed Ethernet network. One microcomputer is dedicated to operation of the detector, control of the camera, and storage of the raw data. The second microcomputer automatically integrates the data as they are collected and allows the user to monitor the quality of data as they are processed. The integration programs are written in Fortran 77 and have been designed to be portable. Additional programs for crystal alignment, detector and camera control, and graphics are written in the C programming language. A description of the system, some characteristics of the detector, and the results of data collection are presented.

The processing of diffraction data taken on a screenless Weissenberg camera for macromolecular crystallography

1989 ◽  
Vol 22 (1) ◽  
pp. 9-18 ◽  
Author(s):  
T. Higashi
Keyword(s):  
Diffraction Data ◽  
Crystal Orientation ◽  
Expansion Method ◽  
Imaging Plate ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Absorption Correction ◽  
Orientation Parameters

A method has been developed based on Rossmann's [J. Appl Cryst. (1979). 12, 225–238] treatment of oscillation camera data for processing of X-ray diffraction data collected on a screenless Weissenberg camera for macromolecular crystals [Sakabe (1983). J. Appl. Cryst. 16, 542–547]. Crystal orientation parameters and film orientation parameters are refined by minimizing the discrepancies between the calculated and observed positions of reflections on a film. A data processing example is presented. Intensities were collected using a synchrotron radiation source and the imaging plate as a detector. The results show that the quality of the data is good, as judged by the agreement of the equivalent reflections. An absorption correction based on the use of the empirical Fourier expansion method reduced the R value and improved the correlations between Bijvoet differences observed on the different imaging plate exposures.

scholarly journals DIALS – a toolbox for diffraction data analysis

2014 ◽  
Vol 70 (a1) ◽  
pp. C1440-C1440 ◽  
Author(s):  
Luis Fuentes-Montero ◽  
James Parkhurst ◽  
Graeme Winter ◽  
David Waterman ◽  
Richard Gildea ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source Software ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
New Methods ◽  
Software Toolbox ◽  
Initial Focus

DIALS is a collaborative initiative to produce an open source software toolbox encompassing all aspects of diffraction data analysis, with an initial focus on X-ray diffraction data from synchrotrons and free-electron lasers for macromolecular crystallography. DIALS [1] has been developed as a modular plug-in framework that permits flexibility not only in the development of new methods and algorithms but also in the application of these methods to data analysis. DIALS builds on the cctbx [2] in addition to its own dedicated tool-kits. We will present the ideas behind DIALS and give examples of its versatility in permitting the use of several spot-finding and indexing schemes, global refinement and both two and three dimensional integration methods.

scholarly journals X-ray Determination of Compressive Residual Stresses in Spring Steel Generated by High-Speed Water Quenching

Materials ◽  
2019 ◽  
Vol 12 (7) ◽  
pp. 1154
Author(s):  
Diego E. Lozano ◽  
George E. Totten ◽  
Yaneth Bedolla-Gil ◽  
Martha Guerrero-Mata ◽  
Marcel Carpio ◽  
...  
Keyword(s):  
Heat Treatment ◽  
Residual Stresses ◽  
High Speed ◽  
Spring Steel ◽  
X Ray Diffraction ◽  
Laboratory Equipment ◽  
X Ray ◽  
Water Chamber ◽  
Hardened Case ◽  
Compressive Residual Stresses

Automotive components manufacturers use the 5160 steel in leaf and coil springs. The industrial heat treatment process consists in austenitizing followed by the oil quenching and tempering process. Typically, compressive residual stresses are induced by shot peening on the surface of automotive springs to bestow compressive residual stresses that improve the fatigue resistance and increase the service life of the parts after heat treatment. In this work, a high-speed quenching was used to achieve compressive residual stresses on the surface of AISI/SAE 5160 steel samples by producing high thermal gradients and interrupting the cooling in order to generate a case-core microstructure. A special laboratory equipment was designed and built, which uses water as the quenching media in a high-speed water chamber. The severity of the cooling was characterized with embedded thermocouples to obtain the cooling curves at different depths from the surface. Samples were cooled for various times to produce different hardened case depths. The microstructure of specimens was observed with a scanning electron microscope (SEM). X-ray diffraction (XRD) was used to estimate the magnitude of residual stresses on the surface of the specimens. Compressive residual stresses at the surface and sub-surface of about −700 MPa were obtained.

scholarly journals High-pressure synthesis and crystal structure of the mixed-cation borate Ga4In4B15O33(OH)3

2019 ◽  
Vol 74 (4) ◽  
pp. 357-363
Author(s):  
Daniela Vitzthum ◽  
Hubert Huppertz
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
High Temperature ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Mixed Cation ◽  
High Pressure High Temperature ◽  
Pressure Synthesis

AbstractThe mixed cation triel borate Ga4In4B15O33(OH)3 was synthesized in a Walker-type multianvil apparatus at high-pressure/high-temperature conditions of 12.5 GPa and 1300°C. Although the product could not be reproduced in further experiments, its crystal structure could be reliably determined via single-crystal X-ray diffraction data. Ga4In4B15O33(OH)3 crystallizes in the tetragonal space group I41/a (origin choice 2) with the lattice parameters a = 11.382(2), c = 15.244(2) Å, and V = 1974.9(4) Å3. The structure of the quaternary triel borate consists of a complex network of BO4 tetrahedra, edge-sharing InO6 octahedra in dinuclear units, and very dense edge-sharing GaO6 octahedra in tetranuclear units.

Crystallization and preliminary x-ray diffraction data of the cryptomonad biliprotein phycocyanin-645 from a Chroomonas spec.

1984 ◽  
Vol 140 (2-3) ◽  
pp. 202-205 ◽  
Author(s):  
Walter Morisset ◽  
Werner Wehrmeyer ◽  
Tilman Schirmer ◽  
Wolfram Bode
Keyword(s):  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray
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