Three-dimensional grain mapping by x-ray diffraction contrast tomography and the use of Friedel pairs in diffraction data analysis

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.

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Structure Refinement of CePtSi and Hydrogenation Behavior of CePdGe, CePtSi and CePtGe

Zeitschrift für Naturforschung B ◽

10.1515/znb-2007-0423 ◽

2007 ◽

Vol 62 (4) ◽

pp. 613-616 ◽

Cited By ~ 8

Author(s):

Wilfried Hermes ◽

Ute Ch. Rodewald ◽

Bernard Chevalier ◽

Rainer Pötgena

Keyword(s):

Single Crystal ◽

Diffraction Data ◽

Structure Refinement ◽

Three Dimensional ◽

Subsequent Annealing ◽

X Ray Diffraction ◽

X Ray ◽

Hydride Formation ◽

Arc Melting ◽

Cerium Compounds

The intermetallic cerium compounds CePdGe, CePtSi, and CePtGe were synthesized from the elements by arc-melting and subsequent annealing. The structure of CePtSi was refined from single crystal X-ray diffraction data: LaPtSi-type (ordered α-ThSi2 version), 141md, a = 419.6(1) and c = 1450.0(5) pm, wR2 = 0.0490, 362 F2 values and 16 variables. The Pt-Si distances within the three-dimensional [PtSi] network are 242 pm, indicating strong Pt-Si interactions. Hydrogenation of the three compounds at 623 K and 4 MPa H2 gave no indication for hydride formation.

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The crystal structure of gersdorffite (III), a distorted and disordered pyrite structure

Mineralogical Magazine and Journal of the Mineralogical Society ◽

10.1180/minmag.1968.283.036.04 ◽

1968 ◽

Vol 36 (283) ◽

pp. 940-947 ◽

Cited By ~ 9

Author(s):

P. Bayliss ◽

N. C. Stephenson

Keyword(s):

Crystal Structure ◽

Metal Atom ◽

Diffraction Data ◽

Three Dimensional ◽

Unit Cell ◽

X Ray Diffraction ◽

Space Group ◽

X Ray ◽

Partially Ordered ◽

The Ideal

SummaryThe crystal structure of gersdorffite (III) has been examined with three-dimensional Weissenberg X-ray diffraction data. The unit cell is isometric with a 5·6849 ± 0·0003 Å, space group PI, and four formula units per cell. This structure has the sulphur and arsenic atoms equally distributed over the non-metal atom sites of pyrite. All atoms show significant random displacements from the ideal pyrite positions to produce triclinic symmetry, which serves to distinguish this mineral from a disordered cubic gersdorffite (II) and a partially ordered cubic gersdorffite (I). Factors responsible for the atomic distortions are discussed.

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AUSPEX: a graphical tool for X-ray diffraction data analysis

Acta Crystallographica Section D Structural Biology ◽

10.1107/s205979831700969x ◽

2017 ◽

Vol 73 (9) ◽

pp. 729-737 ◽

Cited By ~ 5

Author(s):

Andrea Thorn ◽

James Parkhurst ◽

Paul Emsley ◽

Robert A. Nicholls ◽

Melanie Vollmar ◽

...

Keyword(s):

Data Analysis ◽

Diffraction Data ◽

Software Tool ◽

Data Conversion ◽

Data Sets ◽

X Ray Diffraction ◽

X Ray ◽

Pixel Detectors ◽

Graphical Tool ◽

Data Acquisition And Processing

In this paper,AUSPEX, a new software tool for experimental X-ray data analysis, is presented. Exploring the behaviour of diffraction intensities and the associated estimated uncertainties facilitates the discovery of underlying problems and can help users to improve their data acquisition and processing in order to obtain better structural models. The program enables users to inspect the distribution of observed intensities (or amplitudes) against resolution as well as the associated estimated uncertainties (sigmas). It is demonstrated howAUSPEXcan be used to visually and automatically detect ice-ring artefacts in integrated X-ray diffraction data. Such artefacts can hamper structure determination, but may be difficult to identify from the raw diffraction images produced by modern pixel detectors. The analysis suggests that a significant portion of the data sets deposited in the PDB contain ice-ring artefacts. Furthermore, it is demonstrated how other problems in experimental X-ray data caused, for example, by scaling and data-conversion procedures can be detected byAUSPEX.

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D-67 High-Resolution X-ray Diffraction Data Analysis From The Partly Relaxed Semiconductor Structures

Powder Diffraction ◽

10.1154/1.3176000 ◽

2009 ◽

Vol 24 (2) ◽

pp. 171-171

Author(s):

A. Ulyanenkov ◽

A. Benediktovitch ◽

I. Feranchuk ◽

B. He ◽

H. Ress

Keyword(s):

Data Analysis ◽

High Resolution ◽

Diffraction Data ◽

X Ray Diffraction ◽

X Ray ◽

Semiconductor Structures

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A REFINEMENT OF THE CRYSTAL STRUCTURES OF (NH4)2TeBr6 AND Cs2TeBr6

Canadian Journal of Chemistry ◽

10.1139/v66-137 ◽

1966 ◽

Vol 44 (8) ◽

pp. 939-943 ◽

Cited By ~ 40

Author(s):

A. K. Das ◽

I. D. Brown

Keyword(s):

Least Squares ◽

Crystal Structures ◽

Diffraction Data ◽

Bromine Atom ◽

Three Dimensional ◽

X Ray Diffraction ◽

Full Matrix ◽

X Ray ◽

Anisotropic Temperature ◽

Temperature Factors

(NH4)2TeBr6 and Cs2TeBr6 crystals have the cubic K2PtCl6 structure with space group: [Formula: see text] with a0 = 10.728 ± 0.003 Å and 10.918 ± 0.002 Å respectively. The positional coordinate of the bromine atom, and the anisotropic temperature factors of all atoms in the unit cell, have been refined for both crystals by a full matrix least-squares analysis of the three dimensional X-ray diffraction data (R = 0.08). The Te—Br distance, corrected for probable thermal motions of atoms forming the bond, is 2.70 ± 0.01 Å in both crystals.

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X-ray diffraction contrast tomography: a novel technique for three-dimensional grain mapping of polycrystals. II. The combined case

Journal of Applied Crystallography ◽

10.1107/s0021889808001726 ◽

2008 ◽

Vol 41 (2) ◽

pp. 310-318 ◽

Cited By ~ 113

Author(s):

Greg Johnson ◽

Andrew King ◽

Marcelo Goncalves Honnicke ◽

J. Marrow ◽

Wolfgang Ludwig

Keyword(s):

Electron Backscatter Diffraction ◽

Three Dimensional ◽

Real Data ◽

X Ray Diffraction ◽

Data Set ◽

Transmitted Beam ◽

X Ray ◽

Diffraction Contrast ◽

Simultaneous Acquisition ◽

Backscatter Diffraction

By simultaneous acquisition of the transmitted and the diffracted beams, the applicability of the previously introduced diffraction contrast tomography technique [Ludwig, Schmidt, Lauridsen & Poulsen (2008).J. Appl. Cryst.41, 302–309] can be extended to the case of undeformed polycrystalline samples containing more than 100 grains per cross section. The grains are still imaged using the occasionally occurring diffraction contribution to the X-ray attenuation coefficient, which can be observed as a reduction in the intensity of the transmitted beam when a grain fulfils the diffraction condition. Automating the segmentation of the extinction spot images is possible with the additional diffracted beam information, even in the presence of significant spot overlap. By pairing the corresponding direct (`extinction') and diffracted beam spots a robust sorting and indexing approach has been implemented. The analysis procedure is illustrated on a real data set and the result is validated by comparison with a two-dimensional grain map obtained by electron backscatter diffraction.

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The crystal structure of, and the bismuth-copper distribution in synthetic cuprobisrauthite

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1524/zkri.1975.142.3-4.161 ◽

1975 ◽

Vol 142 (3-4) ◽

Cited By ~ 4

Author(s):

T. Ozawa ◽

W. Nowacki

Keyword(s):

Crystal Structure ◽

Diffraction Data ◽

Three Dimensional ◽

X Ray Diffraction ◽

Space Group ◽

X Ray ◽

Copper Distribution

AbstractThe crystal structure of synthetic cuprobismuthite has been determined using three-dimensional x-ray diffraction data. The space group isAll atoms he on mirror planes of the space group at

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The crystal and molecular structure of ovalene: some three-dimensional refinements

Zeitschrift für Kristallographie - Crystalline Materials ◽

10.1524/zkri.1973.137.2-3.159 ◽

1973 ◽

Vol 137 (2-3) ◽

Cited By ~ 3

Author(s):

R. G. Hazell ◽

G. S. Pawley

Keyword(s):

Molecular Structure ◽

Diffraction Data ◽

Crystal And Molecular Structure ◽

Three Dimensional ◽

X Ray Diffraction ◽

X Ray

AbstractThree-dimensional x-ray diffraction data have been taken from ovalene, C

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A complex pseudo-decagonal quasicrystal approximant, Al37(Co,Ni)15.5, solved by rotation electron diffraction

Journal of Applied Crystallography ◽

10.1107/s1600576713029294 ◽

2014 ◽

Vol 47 (1) ◽

pp. 215-221 ◽

Cited By ~ 14

Author(s):

Devinder Singh ◽

Yifeng Yun ◽

Wei Wan ◽

Benjamin Grushko ◽

Xiaodong Zou ◽

...

Keyword(s):

Electron Diffraction ◽

Single Crystal ◽

Diffraction Data ◽

Three Dimensional ◽

Basic Structure ◽

Electron Diffraction Data ◽

Dimensional Electron ◽

X Ray Diffraction ◽

X Ray ◽

Diffraction Patterns

Electron diffraction is a complementary technique to single-crystal X-ray diffraction and powder X-ray diffraction for structure solution of unknown crystals. Crystals too small to be studied by single-crystal X-ray diffraction or too complex to be solved by powder X-ray diffraction can be studied by electron diffraction. The main drawbacks of electron diffraction have been the difficulties in collecting complete three-dimensional electron diffraction data by conventional electron diffraction methods and the very time-consuming data collection. In addition, the intensities of electron diffraction suffer from dynamical scattering. Recently, a new electron diffraction method, rotation electron diffraction (RED), was developed, which can overcome the drawbacks and reduce dynamical effects. A complete three-dimensional electron diffraction data set can be collected from a sub-micrometre-sized single crystal in less than 2 h. Here the RED method is applied forab initiostructure determination of an unknown complex intermetallic phase, the pseudo-decagonal (PD) quasicrystal approximant Al37.0(Co,Ni)15.5, denoted as PD2. RED shows that the crystal is F-centered, witha= 46.4,b= 64.6,c= 8.2 Å. However, as with other approximants in the PD series, the reflections with oddlindices are much weaker than those withleven, so it was decided to first solve the PD2 structure in the smaller, primitive unit cell. The basic structure of PD2 with unit-cell parametersa= 23.2,b= 32.3,c= 4.1 Å and space groupPnmmhas been solved in the present study. The structure withc= 8.2 Å will be taken up in the near future. The basic structure contains 55 unique atoms (17 Co/Ni and 38 Al) and is one of the most complex structures solved by electron diffraction. PD2 is built of characteristic 2 nm wheel clusters with fivefold rotational symmetry, which agrees with results from high-resolution electron microscopy images. Simulated electron diffraction patterns for the structure model are in good agreement with the experimental electron diffraction patterns obtained by RED.

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