scholarly journals Scaling diffraction data in the DIALS software package: algorithms and new approaches for multi-crystal scaling

2020 ◽  
Vol 76 (4) ◽  
pp. 385-399 ◽  
Author(s):  
James Beilsten-Edmands ◽  
Graeme Winter ◽  
Richard Gildea ◽  
James Parkhurst ◽  
David Waterman ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Global Radiation ◽  
Point Group ◽  
Group Symmetry ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
Data Collections ◽  
Free Set ◽  
Scaling Algorithms

In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collections. Scaling corrects for effects such as changes in sample illumination, absorption and, to some extent, global radiation damage that cause the measured intensities of symmetry-equivalent observations to differ throughout a data set. This necessarily requires a prior evaluation of the point-group symmetry of the crystal. This paper describes and evaluates the scaling algorithms implemented within the DIALS data-processing package and demonstrates the effectiveness and key features of the implementation on example macromolecular crystallographic rotation data. In particular, the scaling algorithms enable new workflows for the scaling of multi-crystal or multi-sweep data sets, providing the analysis required to support current trends towards collecting data from ever-smaller samples. In addition, the implementation of a free-set validation method is discussed, which allows the quantification of the suitability of scaling-model and algorithm choices.

scholarly journals Redetermination of the crystal structure of caesium tetrafluoridobromate(III) from single-crystal X-ray diffraction data

IUCrData ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Artem V. Malin ◽  
Sergei I. Ivlev ◽  
Roman V. Ostvald ◽  
Florian Kraus
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Point Group ◽  
Group Symmetry ◽  
Site Symmetry ◽  
X Ray Diffraction ◽  
Cation Site ◽  
X Ray ◽  
Square Planar

Caesium tetrafluoridobromate(III), CsBrF4, was crystallized in form of small blocks by melting and recrystallization. The crystal structure of CsBrF4 was redetermined from single-crystal X-ray diffraction data. In comparison with a previous study based on powder X-ray diffraction data [Ivlev et al. (2013). Z. Anorg. Allg. Chem. 639, 2846–2850], bond lengths and angles were determined with higher precision, and all atoms were refined with anisotropic displacement parameters. It was confirmed that the structure of CsBrF4 contains two square-planar [BrF4]− anions each with point group symmetry mmm, and a caesium cation (site symmetry mm2) that is coordinated by twelve fluorine atoms, forming an anticuboctahedron. CsBrF4 is isotypic with CsAuF4.

Determination of depth profiles from X-ray diffraction data

1993 ◽  
Vol 8 (2) ◽  
pp. 122-126 ◽  
Author(s):  
Paul Predecki
Keyword(s):  
Diffraction Data ◽  
Direct Method ◽  
Sample Surface ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Depth Profiles ◽  
A Direct Method

A direct method is described for determining depth profiles (z-profiles) of diffraction data from experimentally determined τ-profiles, where z is the depth beneath the sample surface and τ is the 1/e penetration depth of the X-ray beam. With certain assumptions, the relation between these two profile functions can be expressed in the form of a Laplace transform. The criteria for fitting experimental τ-data to functions which can be utilized by the method are described. The method was applied to two τ-data sets taken from the literature: (1) of residual strain in an A1 thin film and (2) of residual stress in a surface ground A12O3/5vol% TiC composite. For each data set, it was found that the z-profiles obtained were of two types: oscillatory and nonoscillatory. The nonoscillatory profiles appeared to be qualitatively consistent for a given data set. The oscillatory profiles were considered to be not physically realistic. For the data sets considered, the nonoscillatory z-profiles were found to lie consistently above the corresponding τ-profiles, and to approach the τ-profiles at large z, as expected from the relation between the two.

scholarly journals Redetermination of the crystal structure of β-zinc molybdate from single-crystal X-ray diffraction data

2015 ◽  
Vol 71 (7) ◽  
pp. i6-i7 ◽  
Author(s):  
Olfa Mtioui-Sghaier ◽  
Rafael Mendoza-Meroño ◽  
Lilia Ktari ◽  
Mohamed Dammak ◽  
Santiago García-Granda
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Point Group ◽  
Structure Type ◽  
Group Symmetry ◽  
X Ray Diffraction ◽  
X Ray ◽  
Bond Lengths ◽  
Anisotropic Displacement Parameters

The crystal structure of the β-polymorph of ZnMoO4was re-determined on the basis of single-crystal X-ray diffraction data. In comparison with previous powder X-ray diffraction studies [Katikaneani & Arunachalam (2005).Eur. J. Inorg. Chem. pp. 3080–3087; Cavalcanteet al.(2013).Polyhedron,54, 13–25], all atoms were refined with anisotropic displacement parameters, leading to a higher precision with respect to bond lengths and angles. β-ZnMoO4adopts the wolframite structure type and is composed of distorted ZnO6and MoO6octahedra, both with point group symmetry 2. The distortion of the octahedra is reflected by variation of bond lengths and angles from 2.002 (3)–2.274 (4) Å, 80.63 (11)–108.8 (2)° for equatorial and 158.4 (2)– 162.81 (14)° for axial angles (ZnO6), and of 1.769 (3)–2.171 (3) Å, 73.39 (16)–104.7 (2), 150.8 (2)–164.89 (15)° (MoO6), respectively. In the crystal structure, the same type ofMO6octahedra share edges to built up zigzag chains extending parallel to [001]. The two types of chains are condensed by common vertices into a framework structure. The crystal structure can alternatively be described as derived from a distorted hexagonally closed packed arrangement of the O atoms, with Zn and Mo in half of the octahedral voids.

scholarly journals Background modelling of diffraction data in the presence of ice rings

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 626-638 ◽  
Author(s):  
James M. Parkhurst ◽  
Andrea Thorn ◽  
Melanie Vollmar ◽  
Graeme Winter ◽  
David G. Waterman ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Bragg Reflection ◽  
Background Model ◽  
Data Sets ◽  
Systematic Bias ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Local Background ◽  
Global Background

An algorithm for modelling the background for each Bragg reflection in a series of X-ray diffraction images containing Debye–Scherrer diffraction from ice in the sample is presented. The method involves the use of a global background model which is generated from the complete X-ray diffraction data set. Fitting of this model to the background pixels is then performed for each reflection independently. The algorithm uses a static background model that does not vary over the course of the scan. The greatest improvement can be expected for data where ice rings are present throughout the data set and the local background shape at the size of a spot on the detector does not exhibit large time-dependent variation. However, the algorithm has been applied to data sets whose background showed large pixel variations (variance/mean > 2) and has been shown to improve the results of processing for these data sets. It is shown that the use of a simple flat-background model as in traditional integration programs causes systematic bias in the background determination at ice-ring resolutions, resulting in an overestimation of reflection intensities at the peaks of the ice rings and an underestimation of reflection intensities either side of the ice ring. The new global background-model algorithm presented here corrects for this bias, resulting in a noticeable improvement inRfactors following refinement.

A batch-wise non-linear fitting and analysis tool for treating large X-ray diffraction data sets

2006 ◽  
Vol 39 (2) ◽  
pp. 262-266 ◽  
Author(s):  
R. J. Davies
Keyword(s):  
Diffraction Data ◽  
Operation Mode ◽  
Large Data ◽  
Scattering Data ◽  
Data Sets ◽  
Analysis Tool ◽  
Data Set ◽  
X Ray ◽  
Linear Fitting ◽  
Non Linear

Synchrotron sources offer high-brilliance X-ray beams which are ideal for spatially and time-resolved studies. Large amounts of wide- and small-angle X-ray scattering data can now be generated rapidly, for example, during routine scanning experiments. Consequently, the analysis of the large data sets produced has become a complex and pressing issue. Even relatively simple analyses become difficult when a single data set can contain many thousands of individual diffraction patterns. This article reports on a new software application for the automated analysis of scattering intensity profiles. It is capable of batch-processing thousands of individual data files without user intervention. Diffraction data can be fitted using a combination of background functions and non-linear peak functions. To compliment the batch-wise operation mode, the software includes several specialist algorithms to ensure that the results obtained are reliable. These include peak-tracking, artefact removal, function elimination and spread-estimate fitting. Furthermore, as well as non-linear fitting, the software can calculate integrated intensities and selected orientation parameters.

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.

In Situ Diffraction Studies: Thermal Decomposition of a Natural Plumbojarosite and the Development of Rietveld-Based Data Analysis Techniques

2010 ◽  
Vol 651 ◽  
pp. 37-64 ◽  
Author(s):  
Ian C. Madsen ◽  
Ian E. Grey ◽  
Stuart J. Mills
Keyword(s):  
Thermal Decomposition ◽  
Amorphous Material ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Analysis Techniques ◽  
Path Lengths ◽  
Instrument Configuration

A study of the thermal decomposition sequence of a sample of natural arsenian plumbojarosite has been undertaken using in situ X-ray diffraction. The sample was heated to 900°C using an Anton-Paar heating stage fitted to an INEL CPS120 diffractometer. The data were analysed using a whole-pattern, Rietveld based approach for the extraction of quantitative phase abundances. The instrument configuration used required the development and application of algorithms to correct for aberrations in the (i) peak intensities due to differing path lengths of incident and diffracted beams in the sample and (ii) peak positions due to sample displacement. Details of the structural models used were refined at selected steps in the pattern and then fixed for subsequent analysis. The data sequence consists of some 110 individual data sets which were analysed sequentially with the output of each run forming the input for analysis of the next data set. The results of the analysis show a complex breakdown and recrystallisation sequence including the formation of a major amount of amorphous material after initial breakdown of the plumbojarosite.

Structural Investigations of Colloidal Semiconductor Nanocrystal Heterostructures: Faceting and Epitaxy

1996 ◽  
Vol 452 ◽  
Author(s):  
A. V. Kadavanich ◽  
A. Mews ◽  
S. H. Tolbert ◽  
X. Peng ◽  
M. C. Schlamp ◽  
...  
Keyword(s):  
Point Group ◽  
Group Symmetry ◽  
X Ray Diffraction ◽  
Structural Investigations ◽  
Transmission Microscopy ◽  
Cds Quantum Dot ◽  
Show Evidence ◽  
Multi Wavelength ◽  
Heterogeneous Phase ◽  
Phase Proceeds

AbstractWe use High Resolution Transmission Microscopy (HRTEM) to study CdSe, CdS/HgS/CdS quantum-dot quantum well (QDQW), and CdSe/CdS core-shell nanocrystals, grown by wet-chemical techniques. The nanocrystals have faceted Wulff polyhedron shapes.In addition to HRTEM, we employ multi-wavelength anomalous dispersion (MAD) x-ray diffraction. We use computer modeling to help interpret the experimental data.Growth of a heterogeneous phase proceeds epitaxially preserving the overall shape and point-group symmetry of the original seed nanocrystals, both for wurtzite (CdSe/CdS) and zincblende (CdS/HgS/CdS) type structures.Recently prepared InAs nanocrystals also show evidence of faceting as observed by HRTEM and may lend themselves equally well to epitaxy.

scholarly journals Experiences with making diffraction image data available: what metadata do we need to archive?

2014 ◽  
Vol 70 (10) ◽  
pp. 2502-2509 ◽  
Author(s):  
Loes M. J. Kroon-Batenburg ◽  
John R. Helliwell
Keyword(s):  
Diffraction Data ◽  
Image Data ◽  
Scientific Data ◽  
Data Sets ◽  
Data Archive ◽  
Resolution Limit ◽  
X Ray Diffraction ◽  
Raw Data ◽  
Data Processing Software ◽  
Lysozyme Crystals

Recently, the IUCr (International Union of Crystallography) initiated the formation of a Diffraction Data Deposition Working Group with the aim of developing standards for the representation of raw diffraction data associated with the publication of structural papers. Archiving of raw data serves several goals: to improve the record of science, to verify the reproducibility and to allow detailed checks of scientific data, safeguarding against fraud and to allow reanalysis with future improved techniques. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. In a recent study of the binding of cisplatin and carboplatin to histidine in lysozyme crystals under several conditions, the possible effects of the equipment and X-ray diffraction data-processing software on the occupancies andBfactors of the bound Pt compounds were compared. Initially, 35.3 GB of data were transferred from Manchester to Utrecht to be processed withEVAL. A detailed description and discussion of the availability of metadata was published in a paper that was linked to a local raw data archive at Utrecht University and also mirrored at the TARDIS raw diffraction data archive in Australia. By making these raw diffraction data sets available with the article, it is possible for the diffraction community to make their own evaluation. This led to one of the authors ofXDS(K. Diederichs) to re-integrate the data from crystals that supposedly solely contained bound carboplatin, resulting in the analysis of partially occupied chlorine anomalous electron densities near the Pt-binding sites and the use of several criteria to more carefully assess the diffraction resolution limit. General arguments for archiving raw data, the possibilities of doing so and the requirement of resources are discussed. The problems associated with a partially unknown experimental setup, which preferably should be available as metadata, is discussed. Current thoughts on data compression are summarized, which could be a solution especially for pixel-device data sets with fine slicing that may otherwise present an unmanageable amount of data.

scholarly journals Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystals

2012 ◽  
Vol 46 (1) ◽  
pp. 108-119 ◽  
Author(s):  
Simon W. M. Tanley ◽  
Antoine M. M. Schreurs ◽  
John R. Helliwell ◽  
Loes M. J. Kroon-Batenburg
Keyword(s):  
Diffraction Data ◽  
Data Sets ◽  
X Ray Diffraction ◽  
Noticeable Effect ◽  
Raw Data ◽  
X Ray ◽  
Data Comparison ◽  
Data Processing Software ◽  
Software Packages ◽  
Lysozyme Crystals

The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies andBfactors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed withEVAL. A systematic comparison shows that the largest differences in the occupancies andBfactors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets availableviaa local depository, it is possible for the diffraction community to make their own evaluation as they may wish.

Sign in / Sign up

Export Citation Format

Share Document