|
|
Jon
Agirre
,
Mihaela
Atanasova
,
Haroldas
Bagdonas
,
Charles B.
Ballard
,
Arnaud
Basle
,
James
Beilsten-Edmands
,
Rafael J.
Borges
,
David G.
Brown
,
J. Javier
Burgos-Marmol
,
John M.
Berrisford
,
Paul S.
Bond
,
Iracema
Caballero
,
Lucrezia
Catapano
,
Grzegorz
Chojnowski
,
Atlanta G.
Cook
,
Kevin D.
Cowtan
,
Tristan I.
Croll
,
Judit É.
Debreczeni
,
Nicholas E.
Devenish
,
Eleanor J.
Dodson
,
Tarik R.
Drevon
,
Paul
Emsley
,
Gwyndaf
Evans
,
Phil R.
Evans
,
Maria
Fando
,
James
Foadi
,
Luis
Fuentes-Montero
,
Elspeth F.
Garman
,
Markus
Gerstel
,
Richard J.
Gildea
,
Kaushik
Hatti
,
Maarten L.
Hekkelman
,
Philipp
Heuser
,
Soon Wen
Hoh
,
Michael A.
Hough
,
Huw T.
Jenkins
,
Elisabet
Jiménez
,
Robbie P.
Joosten
,
Ronan M.
Keegan
,
Nicholas
Keep
,
Eugene B.
Krissinel
,
Petr
Kolenko
,
Oleg
Kovalevskiy
,
Victor S.
Lamzin
,
David M.
Lawson
,
Andrey
Lebedev
,
Andrew G. W.
Leslie
,
Bernhard
Lohkamp
,
Fei
Long
,
Martin
Maly
,
Airlie
Mccoy
,
Stuart J.
Mcnicholas
,
Ana
Medina
,
Claudia
Millán
,
James W.
Murray
,
Garib N.
Murshudov
,
Robert A.
Nicholls
,
Martin E. M.
Noble
,
Robert
Oeffner
,
Navraj S.
Pannu
,
James M.
Parkhurst
,
Nicholas
Pearce
,
Joana
Pereira
,
Anastassis
Perrakis
,
Harold R.
Powell
,
Randy J.
Read
,
Daniel J.
Rigden
,
William
Rochira
,
Massimo
Sammito
,
Filomeno
Sanchez Rodriguez
,
George M.
Sheldrick
,
Kathryn L.
Shelley
,
Felix
Simkovic
,
Adam J.
Simpkin
,
Pavol
Skubak
,
Egor
Sobolev
,
Roberto A.
Steiner
,
Kyle
Stevenson
,
Ivo
Tews
,
Jens M. H.
Thomas
,
Andrea
Thorn
,
Josep Triviño
Valls
,
Ville
Uski
,
Isabel
Uson
,
Alexei
Vagin
,
Sameer
Velankar
,
Melanie
Vollmar
,
Helen
Walden
,
David
Waterman
,
Keith S.
Wilson
,
Martyn
Winn
,
Graeme
Winter
,
Marcin
Wojdyr
,
Keitaro
Yamashita
Open Access
Abstract: The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
|
Jun 2023
|
|
|
|
Open Access
Abstract: A computer-aided methodology for the approximate prediction of axially textured polycrystals’ properties is presented. The input data for the developed application consist of: (a) the two-dimensional diffraction pattern of the material under investigation and (b) the tensors of the elasto-piezo-dielectric properties of the single crystal case. Program ANAELU 2.0 allows the determination of the fiber axis inverse pole figure by means of a Rietveld-type procedure. The Material Properties Open Database (MPOD, http://mpod.cimav.edu.mx) provides free access to the experimentally determined values of the tensor properties for several crystal species. Practical estimates of polycrystals’ properties may be obtained by averaging single crystals’ properties tensors, with the orientation distribution function (the symmetry-axis inverse pole figure, in fiber textures) as a weight factor. This treatment, with the application of the Voigt, Reuss and Hill approaches, requires special precautions when it comes to the coupling properties (e.g. piezoelectricity, magnetostriction, magnetoelectricity). Some key physical, mathematical and computational aspects related to the considered topic are discussed. Program GISELLE systematizes the calculation of polycrystal properties under the considered treatments. The application of the proposed methodology to real-world events is illustrated by means of a case study.
|
Jan 2020
|
|
I19-Small Molecule Single Crystal Diffraction
|
Graeme
Winter
,
David G.
Waterman
,
James M.
Parkhurst
,
Aaron S.
Brewster
,
Richard J.
Gildea
,
Markus
Gerstel
,
Luis
Fuentes-Montero
,
Melanie
Vollmar
,
Tara
Michels-Clark
,
Iris D.
Young
,
Nicholas K.
Sauter
,
Gwyndaf
Evans
Open Access
Abstract: The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.
|
Feb 2018
|
|
|
|
Abstract: The estimation of physical properties in textured polycrystals is reviewed. “Principal” properties, which relate actions and responses within the same subsystem (electric, elastic, …), as well as “coupling” properties (e.g., piezomagnetism), linking actions, and responses associated with various subsystems (magneto-elastic, thermo-electric, …) are analyzed. Tensor ranks from 1 to 4, with polar and axial characteristics are considered. Virtual-time inversion (the case of magnetoelectricity) is taken into account. Matrix and surface representations are considered. Significant differences in the effect of texture on properties arise from the diversity of properties tensors ranks and polar/axial natures. To predict the effective values of coupling properties, precautions required for application of the Voigt, Reuss, and Hill approximations are pointed out. At all stages of the proposed methodology, a symmetrized spherical harmonics treatment of the orientation distribution functions, the inverse pole figures and (single- and polycrystals) physical properties is applied. For the case of magnetostriction, a functional program for estimating polycrystal performance is included as Supporting Information. The input data are the single-crystal property coefficients and the polycrystal inverse pole figure parameters. The coincidence of predicted magnetostriction coefficients with experimentally measured values is satisfactory. Recently established considerations regarding the characterization of coupling properties in complex materials are divulged.
|
Nov 2017
|
|
|
|
Open Access
Abstract: 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 in R factors following refinement.
|
Sep 2017
|
|
Data acquisition
Detectors
|
Abstract: In macromolecular crystallography, integration programs - such as DIALS (Waterman et al. 2013) - are used to estimate the
intensities of Bragg reflections recorded on a series of X-ray diffraction images. The reflection intensities are estimated using
the following procedure. A model for the shape of the reflection profile is estimated from a set of strong reflections. This
model is then applied to each reflection in order to estimate the size and shape of the reflection on the detector surface and
to label each pixel as either foreground or background. The intensity of each reflection is then estimated (in the case of
summation integration) by summing the total counts minus the estimated background counts in the foreground region.
Since the background level under the reflection peak cannot be measured directly, it is estimated from the surrounding
background pixels assuming a given model.
|
Aug 2017
|
|
I02-Macromolecular Crystallography
I03-Macromolecular Crystallography
I04-Macromolecular Crystallography
|
Open Access
Abstract: A method for estimating the background under each reflection during integration that is robust in the presence of pixel outliers is presented. The method uses a generalized linear model approach that is more appropriate for use with Poisson distributed data than traditional approaches to pixel outlier handling in integration programs. The algorithm is most applicable to data with a very low background level where assumptions of a normal distribution are no longer valid as an approximation to the Poisson distribution. It is shown that traditional methods can result in the systematic underestimation of background values. This then results in the reflection intensities being overestimated and gives rise to a change in the overall distribution of reflection intensities in a dataset such that too few weak reflections appear to be recorded. Statistical tests performed during data reduction may mistakenly attribute this to merohedral twinning in the crystal. Application of the robust generalized linear model algorithm is shown to correct for this bias.
|
Dec 2016
|
|
|
|
Open Access
Abstract: Currently, an intensive search for high-performance lead-free ferroelectric materials is taking place. ABO3 perovskites (A = Ba, Bi, Ca, K and Na; B = Fe, Nb, Ti, and Zr) appear as promising candidates. Understanding the structure–function relationship is mandatory, and, in this field, the roles of long- and short-range crystal orders and interactions are decisive. In this review, recent advances in the global and local characterization of ferroelectric materials by synchrotron light diffraction, scattering and absorption are analyzed. Single- and poly-crystal synchrotron diffraction studies allow high-resolution investigations regarding the long-range average position of ions and subtle global symmetry break-downs. Ferroelectric materials, under the action of electric fields, undergo crystal symmetry, crystallite/domain orientation distribution and strain condition transformations. Methodological aspects of monitoring these processes are discussed. Two-dimensional diffraction clarify larger scale ordering: polycrystal texture is measured from the intensities distribution along the Debye rings. Local order is investigated by diffuse scattering (DS) and X-ray absorption fine structure (XAFS) experiments. DS provides information about thermal, chemical and displacive low-dimensional disorders. XAFS investigation of ferroelectrics reveals local B-cation off-centering and oxidation state. This technique has the advantage of being element-selective. Representative reports of the mentioned studies are described.
|
Jan 2016
|
|
Data acquisition
|
Open Access
Abstract: Data formats for recording X-ray diffraction data continue to evolve rapidly to accommodate new detector technologies developed in response to more intense light sources. Processing the data from single-crystal X-ray diffraction experiments therefore requires the ability to read, and correctly interpret, image data and metadata from a variety of instruments employing different experimental representations. Tools that have previously been developed to address this problem have been limited either by a lack of extensibility or by inconsistent treatment of image metadata. The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user-extensible approach to reading the data files. The library is written in a mixture of C++ and Python and is distributed as part of the cctbx under an open-source licence at http://cctbx.sourceforge.net .
|
Aug 2014
|
|
Electrical Engineering
Mechanical Engineering
Optics
Theoretical Physics
|
Open Access
Abstract: A description of methods and computer programs for the prediction of “coupling properties” in axially-textured polycrystals is presented. Starting data are the single-crystal properties, texture and stereography. The validity and proper protocols for applying the Voigt, Reuss and Hill approximations to estimate coupling properties effective values is analyzed. Working algorithms for predicting mentioned averages are given. Bunge’s symmetrized spherical harmonics expansion of orientation distribution functions, inverse pole figures and (single and polycrystals) physical properties is applied in all stages of the proposed methodology. The established mathematical route has been systematized in a working computer program. The discussion of piezoelectricity in a representative textured ferro-piezoelectric ceramic illustrates the application of the proposed methodology. Polycrystal coupling properties, predicted by the suggested route, are fairly close to experimentally measured ones.
|
Nov 2013
|
|
