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

2009 ◽  
Vol 80 (3) ◽  
pp. 033905 ◽  
Author(s):  
W. Ludwig ◽  
P. Reischig ◽  
A. King ◽  
M. Herbig ◽  
E. M. Lauridsen ◽  
...  
Keyword(s):  
Data Analysis ◽  
Diffraction Data ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Contrast

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

2007 ◽  
Vol 62 (4) ◽  
pp. 613-616 ◽  
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.

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

1968 ◽  
Vol 36 (283) ◽  
pp. 940-947 ◽  
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.

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

2017 ◽  
Vol 73 (9) ◽  
pp. 729-737 ◽  
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.

scholarly journals Automated harvesting and processing of protein crystals through laser photoablation

2016 ◽  
Vol 72 (4) ◽  
pp. 454-466 ◽  
Author(s):  
Ulrich Zander ◽  
Guillaume Hoffmann ◽  
Irina Cornaciu ◽  
Jean-Pierre Marquette ◽  
Gergely Papp ◽  
...  
Keyword(s):  
Data Collection ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
New Methods ◽  
Repeated Sample ◽  
Sample Recovery ◽  
Through Diffusion ◽  
X Ray Background ◽  
Low X

Currently, macromolecular crystallography projects often require the use of highly automated facilities for crystallization and X-ray data collection. However, crystal harvesting and processing largely depend on manual operations. Here, a series of new methods are presented based on the use of a low X-ray-background film as a crystallization support and a photoablation laser that enable the automation of major operations required for the preparation of crystals for X-ray diffraction experiments. In this approach, the controlled removal of the mother liquor before crystal mounting simplifies the cryocooling process, in many cases eliminating the use of cryoprotectant agents, while crystal-soaking experiments are performed through diffusion, precluding the need for repeated sample-recovery and transfer operations. Moreover, the high-precision laser enables new mounting strategies that are not accessible through other methods. This approach bridges an important gap in automation and can contribute to expanding the capabilities of modern macromolecular crystallography facilities.

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

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

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

1966 ◽  
Vol 44 (8) ◽  
pp. 939-943 ◽  
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.

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

1975 ◽  
Vol 142 (3-4) ◽  
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

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

1973 ◽  
Vol 137 (2-3) ◽  
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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