Open-access and free articles in Acta Crystallographica Section A: Foundations of Crystallography
https://journals.iucr.org/a/journalhomepage.html
Acta Crystallographica Section A: Foundations and Advances covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.en-gbCopyright (c) 2017 International Union of CrystallographyInternational Union of CrystallographyInternational Union of Crystallographyhttps://journals.iucr.orgurn:issn:0108-7673Acta Crystallographica Section A: Foundations and Advances covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.text/htmlOpen-access and free articles in Acta Crystallographica Section A Foundations and Advancestextyearly62002-01-01T00:00+00:00med@iucr.orgActa Crystallographica Section A Foundations and AdvancesCopyright (c) 2017 International Union of Crystallographyurn:issn:0108-7673Open-access and free articles in Acta Crystallographica Section A: Foundations of Crystallographyhttp://journals.iucr.org/logos/rss10a.gif
https://journals.iucr.org/a/journalhomepage.html
Still imageQuasicrystals: What do we know? What do we want to know? What can we know?
http://scripts.iucr.org/cgi-bin/paper?ib5056
More than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Steurer, W.2018-01-01doi:10.1107/S2053273317016540International Union of CrystallographyThe state of the art of quasicrystal research is critically reviewed. Fundamental questions that are still unanswered are discussed and experimental limitations are considered.enQUASICRYSTALS; STRUCTURE ANALYSIS; HIGHER-DIMENSIONAL CRYSTALLOGRAPHY; STABILITY OF QUASICRYSTALS; QUASICRYSTAL GROWTHMore than 35 years and 11 000 publications after the discovery of quasicrystals by Dan Shechtman, quite a bit is known about their occurrence, formation, stability, structures and physical properties. It has also been discovered that quasiperiodic self-assembly is not restricted to intermetallics, but can take place in systems on the meso- and macroscales. However, there are some blank areas, even in the centre of the big picture. For instance, it has still not been fully clarified whether quasicrystals are just entropy-stabilized high-temperature phases or whether they can be thermodynamically stable at 0 K as well. More studies are needed for developing a generally accepted model of quasicrystal growth. The state of the art of quasicrystal research is briefly reviewed and the main as-yet unanswered questions are addressed, as well as the experimental limitations to finding answers to them. The focus of this discussion is on quasicrystal structure analysis as well as on quasicrystal stability and growth mechanisms.text/htmlQuasicrystals: What do we know? What do we want to know? What can we know?text1742018-01-01Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733topical reviews1med@iucr.orgJanuary 2018112053-2733Small-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirements
http://scripts.iucr.org/cgi-bin/paper?vk5021
Small-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349–352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Liebi, M.Georgiadis, M.Kohlbrecher, J.Holler, M.Raabe, J.Usov, I.Menzel, A.Schneider, P.Bunk, O.Guizar-Sicairos, M.2018-01-01doi:10.1107/S205327331701614XInternational Union of CrystallographyThe mathematical framework and reconstruction algorithm for small-angle scattering tensor tomography are introduced in detail, as well as strategies which help to reduce the amount of data and therewith the measurement time required. Experimental validation is provided for the application to trabecular bone.enSMALL-ANGLE X-RAY SCATTERING; TENSOR TOMOGRAPHY; SPHERICAL HARMONICS; BONESmall-angle X-ray scattering tensor tomography, which allows reconstruction of the local three-dimensional reciprocal-space map within a three-dimensional sample as introduced by Liebi et al. [Nature (2015), 527, 349–352], is described in more detail with regard to the mathematical framework and the optimization algorithm. For the case of trabecular bone samples from vertebrae it is shown that the model of the three-dimensional reciprocal-space map using spherical harmonics can adequately describe the measured data. The method enables the determination of nanostructure orientation and degree of orientation as demonstrated previously in a single momentum transfer q range. This article presents a reconstruction of the complete reciprocal-space map for the case of bone over extended ranges of q. In addition, it is shown that uniform angular sampling and advanced regularization strategies help to reduce the amount of data required.text/htmlSmall-angle X-ray scattering tensor tomography: model of the three-dimensional reciprocal-space map, reconstruction algorithm and angular sampling requirementstext1742018-01-01Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733research papers12med@iucr.orgJanuary 2018242053-2733{\bb Z}-module defects in crystals
http://scripts.iucr.org/cgi-bin/paper?td5044
An analysis is presented of the new types of defects that can appear in crystalline structures where the positions of the atoms and the unit cell belong to the same {\bb Z}-module, i.e. are irrational projections of an N > 3-dimensional (N-D) lattice Λ as in the case of quasicrystals. Beyond coherent irrationally oriented twins already discussed in a previous paper [Quiquandon et al. (2016). Acta Cryst. A72, 55–61], new two-dimensional translational defects are expected, the translation vectors of which, being projections of nodes of Λ, have irrational coordinates with respect to the unit-cell reference frame. Partial dislocations, called here module dislocations, are the linear defects bounding these translation faults. A specific case arises when the Burgers vector B is the projection of a non-zero vector of Λ that is perpendicular to the physical space. This new kind of dislocation is called a scalar dislocation since, because its Burgers vector in physical space is zero, it generates no displacement field and has no interaction with external stress fields and other dislocations.https://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Sirindil, A.Quiquandon, M.Gratias, D.2017-10-26doi:10.1107/S2053273317013882International Union of CrystallographyNew kinds of defects can appear in crystals where the atoms and unit cell sit on the nodes of {\bb Z}-modules, i.e. on three-dimensional projections of N-dimensional lattices. These defects are the result of the symmetry breaking due to the projection of the structure from N to three dimensions. Examples are given that illustrate the processes. A new kind of dislocation, here called a `scalar dislocation', is expected; it generates no deformation and has no interaction with stress fields.en{\BB Z}-MODULES; INTERMETALLIC ALLOYS; DEFECTS; TWINS; DISLOCATIONSAn analysis is presented of the new types of defects that can appear in crystalline structures where the positions of the atoms and the unit cell belong to the same {\bb Z}-module, i.e. are irrational projections of an N > 3-dimensional (N-D) lattice Λ as in the case of quasicrystals. Beyond coherent irrationally oriented twins already discussed in a previous paper [Quiquandon et al. (2016). Acta Cryst. A72, 55–61], new two-dimensional translational defects are expected, the translation vectors of which, being projections of nodes of Λ, have irrational coordinates with respect to the unit-cell reference frame. Partial dislocations, called here module dislocations, are the linear defects bounding these translation faults. A specific case arises when the Burgers vector B is the projection of a non-zero vector of Λ that is perpendicular to the physical space. This new kind of dislocation is called a scalar dislocation since, because its Burgers vector in physical space is zero, it generates no displacement field and has no interaction with external stress fields and other dislocations.text/html{\bb Z}-module defects in crystalstext6732017-10-26Acta Crystallographica Section A: Foundations and Advanceshttps://creativecommons.org/licenses/by/2.0/uk2053-2733research papers427med@iucr.orgNovember 20174372053-2733Introducing the holo-TIE approach to cellular imaging
http://scripts.iucr.org/cgi-bin/paper?me0655
Copyright (c) 2017 International Union of Crystallographyurn:issn:2053-2733Robinson, I.2017-06-29doi:10.1107/S2053273317009500International Union of CrystallographyThe new holo-TIE approach to cellular imaging described by Krenkel et al. [Acta Cryst. (2017), A73, 282–292] is discussed.enX-RAY TOMOGRAPHY; COHERENT DIFFRACTION IMAGING; BIOLOGICAL IMAGING; CONTRAST-TRANSFER FUNCTIONtext/htmlIntroducing the holo-TIE approach to cellular imagingtext734Copyright (c) 2017 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2017-06-29281scientific commentaries2053-2733July 2017med@iucr.org2812053-2733High-resolution X-ray diffraction with no sample preparation
http://scripts.iucr.org/cgi-bin/paper?sc5103
It is shown that energy-dispersive X-ray diffraction (EDXRD) implemented in a back-reflection geometry is extremely insensitive to sample morphology and positioning even in a high-resolution configuration. This technique allows high-quality X-ray diffraction analysis of samples that have not been prepared and is therefore completely non-destructive. The experimental technique was implemented on beamline B18 at the Diamond Light Source synchrotron in Oxfordshire, UK. The majority of the experiments in this study were performed with pre-characterized geological materials in order to elucidate the characteristics of this novel technique and to develop the analysis methods. Results are presented that demonstrate phase identification, the derivation of precise unit-cell parameters and extraction of microstructural information on unprepared rock samples and other sample types. A particular highlight was the identification of a specific polytype of a muscovite in an unprepared mica schist sample, avoiding the time-consuming and difficult preparation steps normally required to make this type of identification. The technique was also demonstrated in application to a small number of fossil and archaeological samples. Back-reflection EDXRD implemented in a high-resolution configuration shows great potential in the crystallographic analysis of cultural heritage artefacts for the purposes of scientific research such as provenancing, as well as contributing to the formulation of conservation strategies. Possibilities for moving the technique from the synchrotron into museums are discussed. The avoidance of the need to extract samples from high-value and rare objects is a highly significant advantage, applicable also in other potential research areas such as palaeontology, and the study of meteorites and planetary materials brought to Earth by sample-return missions.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Hansford, G.M.Turner, S.M.R.Degryse, P.Shortland, A.J.2017-06-29doi:10.1107/S2053273317008592International Union of CrystallographyA novel, high-resolution X-ray diffraction (XRD) technique that provides completely non-destructive, high-quality XRD analyses of unprepared samples is demonstrated. The method shows great potential in the characterization of cultural heritage artefacts.enENERGY-DISPERSIVE XRD; BACK-REFLECTION GEOMETRY; SAMPLE PREPARATION; NON-DESTRUCTIVE ANALYSIS; CULTURAL HERITAGE ARTEFACTS; SYNCHROTRON EXPERIMENTSIt is shown that energy-dispersive X-ray diffraction (EDXRD) implemented in a back-reflection geometry is extremely insensitive to sample morphology and positioning even in a high-resolution configuration. This technique allows high-quality X-ray diffraction analysis of samples that have not been prepared and is therefore completely non-destructive. The experimental technique was implemented on beamline B18 at the Diamond Light Source synchrotron in Oxfordshire, UK. The majority of the experiments in this study were performed with pre-characterized geological materials in order to elucidate the characteristics of this novel technique and to develop the analysis methods. Results are presented that demonstrate phase identification, the derivation of precise unit-cell parameters and extraction of microstructural information on unprepared rock samples and other sample types. A particular highlight was the identification of a specific polytype of a muscovite in an unprepared mica schist sample, avoiding the time-consuming and difficult preparation steps normally required to make this type of identification. The technique was also demonstrated in application to a small number of fossil and archaeological samples. Back-reflection EDXRD implemented in a high-resolution configuration shows great potential in the crystallographic analysis of cultural heritage artefacts for the purposes of scientific research such as provenancing, as well as contributing to the formulation of conservation strategies. Possibilities for moving the technique from the synchrotron into museums are discussed. The avoidance of the need to extract samples from high-value and rare objects is a highly significant advantage, applicable also in other potential research areas such as palaeontology, and the study of meteorites and planetary materials brought to Earth by sample-return missions.text/htmlHigh-resolution X-ray diffraction with no sample preparationtext734http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2017-06-29293research papers2053-2733July 2017med@iucr.org3112053-2733Three-dimensional single-cell imaging with X-ray waveguides in the holographic regime
http://scripts.iucr.org/cgi-bin/paper?ib5053
X-ray tomography at the level of single biological cells is possible in a low-dose regime, based on full-field holographic recordings, with phase contrast originating from free-space wave propagation. Building upon recent progress in cellular imaging based on the illumination by quasi-point sources provided by X-ray waveguides, here this approach is extended in several ways. First, the phase-retrieval algorithms are extended by an optimized deterministic inversion, based on a multi-distance recording. Second, different advanced forms of iterative phase retrieval are used, operational for single-distance and multi-distance recordings. Results are compared for several different preparations of macrophage cells, for different staining and labelling. As a result, it is shown that phase retrieval is no longer a bottleneck for holographic imaging of cells, and how advanced schemes can be implemented to cope also with high noise and inconsistencies in the data.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Krenkel, M.Toepperwien, M.Alves, F.Salditt, T.2017-06-29doi:10.1107/S2053273317007902International Union of CrystallographyPhase-contrast X-ray imaging of biological cells in two and three dimensions can be carried out with a low dose, based on free propagation and a setting of optimized wavefronts in cone-beam geometry. In order to reach the required contrast level, images have to be recorded in the holographic regime. The main result of this work is holographic recordings of a quality that is fully amenable to quantitative phase retrieval, beyond previous approximations. Different approaches to sample preparations, data recording and phase retrieval are compared.enX-RAY HOLOGRAPHY; PHASE RETRIEVAL; X-RAY TOMOGRAPHY; X-RAY WAVEGUIDES; COHERENT IMAGINGX-ray tomography at the level of single biological cells is possible in a low-dose regime, based on full-field holographic recordings, with phase contrast originating from free-space wave propagation. Building upon recent progress in cellular imaging based on the illumination by quasi-point sources provided by X-ray waveguides, here this approach is extended in several ways. First, the phase-retrieval algorithms are extended by an optimized deterministic inversion, based on a multi-distance recording. Second, different advanced forms of iterative phase retrieval are used, operational for single-distance and multi-distance recordings. Results are compared for several different preparations of macrophage cells, for different staining and labelling. As a result, it is shown that phase retrieval is no longer a bottleneck for holographic imaging of cells, and how advanced schemes can be implemented to cope also with high noise and inconsistencies in the data.text/htmlThree-dimensional single-cell imaging with X-ray waveguides in the holographic regimetext734http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2017-06-29282research papers2053-2733July 2017med@iucr.org2922053-2733On the Penrose and Taylor–Socolar hexagonal tilings
http://scripts.iucr.org/cgi-bin/paper?ae5032
The intimate relationship between the Penrose and the Taylor–Socolar tilings is studied, within both the context of double hexagon tiles and the algebraic context of hierarchical inverse sequences of triangular lattices. This unified approach produces both types of tilings together, clarifies their relationship and offers straightforward proofs of their basic properties.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Lee, J.-Y.Moody, R.V.2017-05-07doi:10.1107/S2053273317003576International Union of CrystallographyA uniform geometric/algebraic approach to the Penrose and Taylor–Socolar hexagonal tilings is given, which clarifies their construction and the way in which they are inter-related.enPENROSE TILING; TAYLOR-SOCOLAR TILING; DOUBLE HEXAGON TILING; NESTED TRIANGULARIZATIONS; INVERSE SEQUENCES OF HIERARCHICAL LATTICESThe intimate relationship between the Penrose and the Taylor–Socolar tilings is studied, within both the context of double hexagon tiles and the algebraic context of hierarchical inverse sequences of triangular lattices. This unified approach produces both types of tilings together, clarifies their relationship and offers straightforward proofs of their basic properties.text/htmlOn the Penrose and Taylor–Socolar hexagonal tilingstext733http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2017-05-07246research papers2053-2733May 2017med@iucr.org2562053-2733Approximating coincidence – turning a new page for bicrystallography
http://scripts.iucr.org/cgi-bin/paper?me0642
Copyright (c) 2017 International Union of Crystallographyurn:issn:2053-2733Patala, S.2017-03-01doi:10.1107/S2053273317003321International Union of CrystallographyThe wider significance of the regularized and physically intuitive Σ function developed by Runnels [Acta Cryst. (2017), A73, 87–92] is discussed.enBICRYSTALLOGRAPHY; COINCIDENCE SITE LATTICE; INTERFACEStext/htmlApproximating coincidence – turning a new page for bicrystallographytext2732017-03-01Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2017 International Union of Crystallography2053-2733scientific commentaries85med@iucr.orgMarch 2017862053-2733Report of the Executive Committee for 2015
http://scripts.iucr.org/cgi-bin/paper?es0419
The report of the Executive Committee for 2015 is presented.Copyright (c) 2017 International Union of Crystallographyurn:issn:2053-2733Dacombe, M.2017-02-13doi:10.1107/S2053273316011128International Union of CrystallographyThe report of the Executive Committee for 2015 is presented.enINTERNATIONAL UNION OF CRYSTALLOGRAPHY; EXECUTIVE COMMITTEEThe report of the Executive Committee for 2015 is presented.text/htmlReport of the Executive Committee for 2015text2732017-02-13Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2017 International Union of Crystallography2053-2733international union of crystallography159med@iucr.orgMarch 20171992053-2733To superspace and beyond
http://scripts.iucr.org/cgi-bin/paper?me0636
Copyright (c) 2017 International Union of Crystallographyurn:issn:2053-2733Senn, M.S.2017-01-01doi:10.1107/S2053273316019902International Union of CrystallographyThe significance of an algorithm developed by H. T. Stokes & B. J. Campbell [Acta Cryst. (2017), A73, 4–13] is discussed. The algorithm promises to be a key tool for understanding the structure–property relationships of the many technologically important materials that display incommensurate modulations in their atomic and/or magnetic structure.enSTRUCTURE-PROPERTY RELATIONSHIPS; SUPERSPACE; INCOMMENSURATE STRUCTURES; IRREDUCIBLE REPRESENTATIONS; CHARGE-DENSITY WAVES; PHASE TRANSITIONStext/htmlTo superspace and beyondtext1732017-01-01Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2017 International Union of Crystallography2053-2733scientific commentaries1med@iucr.orgJanuary 201732053-2733Asymmetry in serial femtosecond crystallography data
http://scripts.iucr.org/cgi-bin/paper?mq5047
Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of the Blastochloris viridis photosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Sharma, A.Johansson, L.Dunevall, E.Wahlgren, W.Neutze, R.Katona, G.2017-01-30doi:10.1107/S2053273316018696International Union of CrystallographyDistribution analysis of intensity observations in serial femtosecond crystallography data processing helps to separate Bragg reflections from the background detector response.enEX-GAUSSIAN DISTRIBUTION; SERIAL FEMTOSECOND CRYSTALLOGRAPHY; BRAGG REFLECTIONS; SYSTEMATIC ABSENCES; INTENSITY DISTRIBUTIONSerial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of the Blastochloris viridis photosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background.text/htmlAsymmetry in serial femtosecond crystallography datatext2732017-01-30Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers93med@iucr.orgMarch 20171012053-2733Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm
http://scripts.iucr.org/cgi-bin/paper?sc5096
An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationship of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733He, H.Fang, H.Miller, M.D.Phillips Jr, G.N.Su, W.-P.2016-07-15doi:10.1107/S2053273316010731International Union of CrystallographyAn iterative transform algorithm is proposed to improve the conventional molecular-replacement method for solving the phase problem in X-ray crystallography. Several examples of successful trial calculations carried out with real diffraction data are presented.enMOLECULAR REPLACEMENT; HYBRID INPUT-OUTPUT ALGORITHM; AB INITIO PHASING; PROTEIN CRYSTALLOGRAPHYAn iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationship of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.text/htmlImproving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithmtext725http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2016-07-15539research papers2053-2733September 2016med@iucr.org5472053-2733Simple graphs that guide combinatorial materials design
http://scripts.iucr.org/cgi-bin/paper?me0618
Copyright (c) 2016 International Union of Crystallographyurn:issn:2053-2733Duxbury, P.M.2016-04-29doi:10.1107/S2053273316006811International Union of CrystallographyThe representation of crystal structures by nets provides a useful framework for thinking about the design of new materials.enQUOTIENT GRAPHS; RETICULAR CHEMISTRY; CRYSTAL TOPOLOGY; MATERIALS DESIGNtext/htmlSimple graphs that guide combinatorial materials designtext723Copyright (c) 2016 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2016-04-29265scientific commentaries2053-2733May 2016med@iucr.org2672053-2733Estimating the difference between structure-factor amplitudes using multivariate Bayesian inference
http://scripts.iucr.org/cgi-bin/paper?mq5040
In experimental research referencing two or more measurements to one another is a powerful tool to reduce the effect of systematic errors between different sets of measurements. The interesting quantity is usually derived from two measurements on the same sample under different conditions. While an elaborate experimental design is essential for improving the estimate, the data analysis should also maximally exploit the covariance between the measurements. In X-ray crystallography the difference between structure-factor amplitudes carries important information to solve experimental phasing problems or to determine time-dependent structural changes in pump–probe experiments. Here a multivariate Bayesian method was used to analyse intensity measurement pairs to determine their underlying structure-factor amplitudes and their differences. The posterior distribution of the model parameter was approximated with a Markov chain Monte Carlo algorithm. The described merging method is shown to be especially advantageous when systematic and random errors result in recording negative intensity measurements.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Katona, G.Garcia-Bonete, M.-J.Lundholm, I.V.2016-03-30doi:10.1107/S2053273316003430International Union of CrystallographyA Bayesian model which uses a Markov chain Monte Carlo algorithm has been developed to estimate structure-factor amplitude differences.enEXPERIMENTAL PHASING; SELF-REFERENCING; BAYESIAN MODEL; TIME-RESOLVED CRYSTALLOGRAPHY; MARKOV CHAIN MONTE CARLO ALGORITHMIn experimental research referencing two or more measurements to one another is a powerful tool to reduce the effect of systematic errors between different sets of measurements. The interesting quantity is usually derived from two measurements on the same sample under different conditions. While an elaborate experimental design is essential for improving the estimate, the data analysis should also maximally exploit the covariance between the measurements. In X-ray crystallography the difference between structure-factor amplitudes carries important information to solve experimental phasing problems or to determine time-dependent structural changes in pump–probe experiments. Here a multivariate Bayesian method was used to analyse intensity measurement pairs to determine their underlying structure-factor amplitudes and their differences. The posterior distribution of the model parameter was approximated with a Markov chain Monte Carlo algorithm. The described merging method is shown to be especially advantageous when systematic and random errors result in recording negative intensity measurements.text/htmlEstimating the difference between structure-factor amplitudes using multivariate Bayesian inferencetext723http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2016-03-30406short communications2053-2733May 2016med@iucr.org4112053-2733Cryo-coherent diffractive imaging of biological samples with X-ray free-electron lasers
http://scripts.iucr.org/cgi-bin/paper?me0612
Recent developments in the imaging of biological samples using the X-ray free-electron laser at the SACLA facility are highlighted.Copyright (c) 2016 International Union of Crystallographyurn:issn:2053-2733Jiang, H.2016-02-26doi:10.1107/S2053273316003107International Union of CrystallographyRecent developments in the imaging of biological samples using the X-ray free-electron laser at the SACLA facility are highlighted.enX-RAY FREE-ELECTRON LASERS; CRYO-COHERENT DIFFRACTIVE IMAGING; CDI; XFELS; BIOLOGICAL SPECIMENSRecent developments in the imaging of biological samples using the X-ray free-electron laser at the SACLA facility are highlighted.text/htmlCryo-coherent diffractive imaging of biological samples with X-ray free-electron laserstext722Copyright (c) 2016 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2016-02-26177scientific commentaries2053-2733March 2016med@iucr.org1782053-2733On the possibility of using X-ray Compton scattering to study magnetoelectrical properties of crystals
http://scripts.iucr.org/cgi-bin/paper?kx5049
This paper discusses the possibility of using Compton scattering – an inelastic X-ray scattering process that yields a projection of the electron momentum density – to probe magnetoelectrical properties. It is shown that an antisymmetric component of the momentum density is a unique fingerprint of such time- and parity-odd physics. It is argued that polar ferromagnets are ideal candidates to demonstrate this phenomenon and the first experimental results are shown, on a single-domain crystal of GaFeO3. The measured antisymmetric Compton profile is very small (≃ 10−5 of the symmetric part) and of the same order of magnitude as the statistical errors. Relativistic first-principles simulations of the antisymmetric Compton profile are presented and it is shown that, while the effect is indeed predicted by theory, and scales with the size of the valence spin–orbit interaction, its magnitude is significantly overestimated. The paper outlines some important constraints on the properties of the antisymmetric Compton profile arising from the underlying crystallographic symmetry of the sample.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Collins, S.P.Laundy, D.Connolley, T.van der Laan, G.Fabrizi, F.Janssen, O.Cooper, M.J.Ebert, H.Mankovsky, S.2016-02-16doi:10.1107/S2053273316000863International Union of CrystallographyThe possibility of using X-ray Compton scattering to reveal antisymmetric components of the electron momentum density, as a fingerprint of magnetoelectric sample properties, is investigated experimentally and theoretically by studying the polar ferromagnet GaFeO3.enCOMPTON SCATTERING; MAGNETOELECTRIC PROPERTIES; SYNCHROTRON RADIATION; DENSITY FUNCTIONAL THEORY; DFT; KORRINGA-KOHN-ROSTOKER (KKR) GREEN'S FUNCTION METHOD; KKR METHODThis paper discusses the possibility of using Compton scattering – an inelastic X-ray scattering process that yields a projection of the electron momentum density – to probe magnetoelectrical properties. It is shown that an antisymmetric component of the momentum density is a unique fingerprint of such time- and parity-odd physics. It is argued that polar ferromagnets are ideal candidates to demonstrate this phenomenon and the first experimental results are shown, on a single-domain crystal of GaFeO3. The measured antisymmetric Compton profile is very small (≃ 10−5 of the symmetric part) and of the same order of magnitude as the statistical errors. Relativistic first-principles simulations of the antisymmetric Compton profile are presented and it is shown that, while the effect is indeed predicted by theory, and scales with the size of the valence spin–orbit interaction, its magnitude is significantly overestimated. The paper outlines some important constraints on the properties of the antisymmetric Compton profile arising from the underlying crystallographic symmetry of the sample.text/htmlOn the possibility of using X-ray Compton scattering to study magnetoelectrical properties of crystalstext722http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2016-02-16197research papers2053-2733March 2016med@iucr.org2052053-2733Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy
http://scripts.iucr.org/cgi-bin/paper?mq5039
Coherent X-ray diffraction imaging at cryogenic temperature (cryo-CXDI) allows the analysis of internal structures of unstained, non-crystalline, whole biological samples in micrometre to sub-micrometre dimensions. Targets include cells and cell organelles. This approach involves preparing frozen-hydrated samples under controlled humidity, transferring the samples to a cryo-stage inside a vacuum chamber of a diffractometer, and then exposing the samples to coherent X-rays. Since 2012, cryo-coherent diffraction imaging (CDI) experiments have been carried out with the X-ray free-electron laser (XFEL) at the SPring-8 Ångstrom Compact free-electron LAser (SACLA) facility in Japan. Complementary use of cryo-electron microscopy and/or light microscopy is highly beneficial for both pre-checking samples and studying the integrity or nature of the sample. This article reports the authors' experience in cryo-XFEL-CDI of biological cells and organelles at SACLA, and describes an attempt towards reliable and higher-resolution reconstructions, including signal enhancement with strong scatterers and Patterson-search phasing.Copyright (c) 2016 International Union of Crystallographyurn:issn:2053-2733Takayama, Y.Yonekura, K.2016-01-29doi:10.1107/S2053273315023980International Union of CrystallographyCryogenic coherent X-ray diffraction imaging can be used for structural analysis of unstained, non-crystalline, whole biological samples such as cells and cell organelles. This article reports on current and future applications of cryo-coherent diffraction imaging with the X-ray free-electron laser (XFEL) at the Japanese XFEL facility, SACLA, and demonstrates the merit of a correlative approach with cryo-electron and light microscopy.enCOHERENT X-RAY DIFFRACTION IMAGING; X-RAY FREE-ELECTRON LASERS; FROZEN-HYDRATED NON-CRYSTALLINE SAMPLES; STRUCTURAL ANALYSIS; CORRELATIVE MICROSCOPYCoherent X-ray diffraction imaging at cryogenic temperature (cryo-CXDI) allows the analysis of internal structures of unstained, non-crystalline, whole biological samples in micrometre to sub-micrometre dimensions. Targets include cells and cell organelles. This approach involves preparing frozen-hydrated samples under controlled humidity, transferring the samples to a cryo-stage inside a vacuum chamber of a diffractometer, and then exposing the samples to coherent X-rays. Since 2012, cryo-coherent diffraction imaging (CDI) experiments have been carried out with the X-ray free-electron laser (XFEL) at the SPring-8 Ångstrom Compact free-electron LAser (SACLA) facility in Japan. Complementary use of cryo-electron microscopy and/or light microscopy is highly beneficial for both pre-checking samples and studying the integrity or nature of the sample. This article reports the authors' experience in cryo-XFEL-CDI of biological cells and organelles at SACLA, and describes an attempt towards reliable and higher-resolution reconstructions, including signal enhancement with strong scatterers and Patterson-search phasing.text/htmlCryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopytext722Copyright (c) 2016 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2016-01-29179feature articles2053-2733March 2016med@iucr.org1892053-2733Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector
http://scripts.iucr.org/cgi-bin/paper?td5026
Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014).http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733van Genderen, E.Clabbers, M.T.B.Das, P.P.Stewart, A.Nederlof, I.Barentsen, K.C.Portillo, Q.Pannu, N.S.Nicolopoulos, S.Gruene, T.Abrahams, J.P.2016-02-05doi:10.1107/S2053273315022500International Union of CrystallographyA specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods.enELECTRON NANOCRYSTALLOGRAPHY; TIMEPIX QUANTUM AREA DETECTOR; CARBAMAZEPINE; NICOTINIC ACID; ELECTRON DIFFRACTION STRUCTURE DETERMINATIONUntil recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014).text/htmlAb initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detectortext722http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2016-02-05236research papers2053-2733March 2016med@iucr.org2422053-2733Three-dimensional propagation in near-field tomographic X-ray phase retrieval
http://scripts.iucr.org/cgi-bin/paper?mq5036
This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Ruhlandt, A.Salditt, T.2016-01-29doi:10.1107/S2053273315022469International Union of CrystallographyAn extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions is presented, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints.enTOMOGRAPHY; PHASE RETRIEVAL; X-RAY IMAGINGThis paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.text/htmlThree-dimensional propagation in near-field tomographic X-ray phase retrievaltext722http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2016-01-29215research papers2053-2733March 2016med@iucr.org2212053-2733What is an `ideally imperfect' crystal? Is kinematical theory appropriate?
http://scripts.iucr.org/cgi-bin/paper?ae5011
Most materials are crystalline because atoms and molecules tend to form ordered arrangements, and since the interatomic distances are comparable with the wavelength of X-rays, their interaction creates diffraction patterns. The intensity in these patterns changes with crystal quality. Perfect crystals, e.g. semiconductors, fit well to dynamical theory, whereas crystals that reveal the stereochemistry of complex biological molecules, the structure of organic and inorganic molecules and powders are required to be fragmented (termed `ideally imperfect') to justify the use of the simpler kinematical theory. New experimental results of perfect and imperfect crystals are interpreted with a fundamental description of diffraction, which does not need fragmented crystals but just ubiquitous defects. The distribution of the intensity is modified and can influence the interpretation of the patterns.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fewster, P.F.2016-01-01doi:10.1107/S2053273315018975International Union of CrystallographyThe diffraction from imperfect crystals and the applicability of kinematical theory are described.enIMPERFECT CRYSTALS; KINEMATICAL THEORY; DYNAMICAL THEORYMost materials are crystalline because atoms and molecules tend to form ordered arrangements, and since the interatomic distances are comparable with the wavelength of X-rays, their interaction creates diffraction patterns. The intensity in these patterns changes with crystal quality. Perfect crystals, e.g. semiconductors, fit well to dynamical theory, whereas crystals that reveal the stereochemistry of complex biological molecules, the structure of organic and inorganic molecules and powders are required to be fragmented (termed `ideally imperfect') to justify the use of the simpler kinematical theory. New experimental results of perfect and imperfect crystals are interpreted with a fundamental description of diffraction, which does not need fragmented crystals but just ubiquitous defects. The distribution of the intensity is modified and can influence the interpretation of the patterns.text/htmlWhat is an `ideally imperfect' crystal? Is kinematical theory appropriate?text1722016-01-01Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers50med@iucr.org542053-2733Merohedral twins revisited: quinary twins and beyond
http://scripts.iucr.org/cgi-bin/paper?pc5056
A twin is defined as being an external operation between two identical crystals that share a fraction of the atomic structure with no discontinuity from one crystal to the other. This includes merohedral twins, twins by reticular merohedry as well as coherent twins by contact where only the habit plane is shared by the two adjacent crystals (epitaxy). Interesting and original cases appear when the invariant substructure is built with positions belonging to the same {\bb Z}-module as, for example, the quinary twin structure first drawn by Albrecht Dürer [(1525). The Painter's Manual: a Manual of Measurement of Lines, Areas and Solids by Means of Compass and Ruler. Facsimile Edition (1977), translated with commentary by W. L. Strauss. New York: Abaris Books]. This paper will show that the Dürer twins, once defined in five-dimensional space, are simple merohedral twins, in the sense of Georges Friedel, leaving the five-dimensional lattice invariant. This analysis will be generalized to some other higher-order {\bb Z}-modules.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Quiquandon, M.Gratias, D.Sirindil, A.Portier, R.2016-01-01doi:10.1107/S2053273315018197International Union of CrystallographyThe generalization of lattice invariance in merohedral twins to {\bb Z}-module invariance is discussed.enMEROHEDRAL TWINS; QUINARY TWINS; DURER STRUCTURE; POLYGONAL TILINGSA twin is defined as being an external operation between two identical crystals that share a fraction of the atomic structure with no discontinuity from one crystal to the other. This includes merohedral twins, twins by reticular merohedry as well as coherent twins by contact where only the habit plane is shared by the two adjacent crystals (epitaxy). Interesting and original cases appear when the invariant substructure is built with positions belonging to the same {\bb Z}-module as, for example, the quinary twin structure first drawn by Albrecht Dürer [(1525). The Painter's Manual: a Manual of Measurement of Lines, Areas and Solids by Means of Compass and Ruler. Facsimile Edition (1977), translated with commentary by W. L. Strauss. New York: Abaris Books]. This paper will show that the Dürer twins, once defined in five-dimensional space, are simple merohedral twins, in the sense of Georges Friedel, leaving the five-dimensional lattice invariant. This analysis will be generalized to some other higher-order {\bb Z}-modules.text/htmlMerohedral twins revisited: quinary twins and beyondtext1722016-01-01Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers55med@iucr.org612053-2733Computation in electron microscopy
http://scripts.iucr.org/cgi-bin/paper?mq5037
Some uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.Copyright (c) 2016 International Union of Crystallographyurn:issn:2053-2733Kirkland, E.J.2016-01-01doi:10.1107/S205327331501757XInternational Union of CrystallographyThe numerical computation of high-resolution transmission electron micrographs from first principles and its inverse are surveyed.enHIGH-RESOLUTION TRANSMISSION ELECTRON MICROSCOPY; HRTEM; MULTISLICE METHOD; EXIT-WAVE RECONSTRUCTION; DECONVOLUTIONSome uses of the computer and computation in high-resolution transmission electron microscopy are reviewed. The theory of image calculation using Bloch wave and multislice methods with and without aberration correction is reviewed and some applications are discussed. The inverse problem of reconstructing the specimen structure from an experimentally measured electron microscope image is discussed. Some future directions of software development are given.text/htmlComputation in electron microscopytext1722016-01-01Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2016 International Union of Crystallography2053-2733lead articles1med@iucr.org272053-2733Distribution rules of systematic absences on the Conway topograph and their application to powder auto-indexing: erratum
http://scripts.iucr.org/cgi-bin/paper?sc5092
A correction is made to the article by Oishi-Tomiyasu [Acta Cryst. (2013), A69, 603–610].Copyright (c) 2015 International Union of Crystallographyurn:issn:2053-2733Oishi-Tomiyasu, R.2015-10-06doi:10.1107/S2053273315015065International Union of CrystallographyA correction is made to the article by Oishi-Tomiyasu [Acta Cryst. (2013), A69, 603–610].enSYSTEMATIC ABSENCES; POWDER AUTO-INDEXING; ALGORITHMA correction is made to the article by Oishi-Tomiyasu [Acta Cryst. (2013), A69, 603–610].text/htmlDistribution rules of systematic absences on the Conway topograph and their application to powder auto-indexing: erratumtext6712015-10-06Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2015 International Union of Crystallography2053-2733addenda and errata628med@iucr.org6282053-2733Report of the Executive Committee for 2014
http://scripts.iucr.org/cgi-bin/paper?es0412
The report of the Executive Committee for 2014 is presented.urn:issn:2053-2733Dacombe, M.2016-03-14doi:10.1107/S2053273315012863International Union of CrystallographyThe report of the Executive Committee for 2014 is presented.enEXECUTIVE COMMITTEEThe report of the Executive Committee for 2014 is presented.text/htmlReport of the Executive Committee for 2014text723Acta Crystallographica Section A: Foundations and Advances2016-03-14412international union of crystallography2053-2733May 2016med@iucr.org4552053-2733Accessible atomic structures from sub-micron protein crystals
http://scripts.iucr.org/cgi-bin/paper?me0583
Copyright (c) 2015 International Union of Crystallographyurn:issn:2053-2733Rodriguez, J.A.2015-07-01doi:10.1107/S2053273315012206International Union of CrystallographyA guide to the collection and processing of MicroED data invites X-ray crystallographers and electron microscopists to solve atomic structures from tiny protein crystals.enMICROED; NANOCRYSTALS; ELECTRON DIFFRACTIONtext/htmlAccessible atomic structures from sub-micron protein crystalstext4712015-07-01Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2015 International Union of Crystallography2053-2733scientific commentaries351med@iucr.org3522053-2733MicroED data collection and processing
http://scripts.iucr.org/cgi-bin/paper?mq5031
MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Hattne, J.Reyes, F.E.Nannenga, B.L.Shi, D.de la Cruz, M.J.Leslie, A.G.W.Gonen, T.2015-07-01doi:10.1107/S2053273315010669International Union of CrystallographyThe collection and processing of MicroED data are presented.enMICROED; ELECTRON DIFFRACTION; CRYSTALLOGRAPHY; CRYO-EM; NANOCRYSTALSMicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.text/htmlMicroED data collection and processingtext4712015-07-01Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733feature articles353med@iucr.org3602053-2733Identification of inversion domains in KTiOPO4 via resonant X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?pc5051
A novel method is presented for the identification of the absolute crystallographic structure in multi-domain polar materials such as ferroelectric KTiOPO4. Resonant (or `anomalous') X-ray diffraction spectra collected across the absorption K edge of Ti (4.966 keV) on a single Bragg reflection demonstrate a huge intensity ratio above and below the edge, providing a polar domain contrast of ∼270. This allows one to map the spatial domain distribution in a periodically inverted sample, with a resolution of ∼1 µm achieved with a microfocused beam. This non-contact, non-destructive technique is well suited for samples of large dimensions (in contrast with traditional resonant X-ray methods based on diffraction from Friedel pairs), and its potential is particularly relevant in the context of physical phenomena connected with an absence of inversion symmetry, which require characterization of the underlying absolute atomic structure (such as in the case of magnetoelectric coupling and multiferroics).http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fabrizi, F.Thomas, P.A.Nisbet, G.Collins, S.P.2015-05-14doi:10.1107/S2053273315007238International Union of CrystallographyThe identification and high-resolution mapping of the absolute crystallographic structure in multi-domain ferroelectric KTiOPO4 is achieved through a novel synchrotron X-ray diffraction method. On a single Bragg reflection, the intensity ratio in resonant diffraction below and above the Ti absorption K edge demonstrates a domain contrast up to a factor of ∼270, thus implementing a non-contact, non-destructive imaging technique with micrometre spatial resolution, applicable to samples of arbitrarily large dimensions.enRESONANT X-RAY DIFFRACTION; SYNCHROTRON RADIATION; IMAGING; ABSOLUTE STRUCTURE; INVERSION SYMMETRY; INVERSION DOMAINS; FERROELECTRICSA novel method is presented for the identification of the absolute crystallographic structure in multi-domain polar materials such as ferroelectric KTiOPO4. Resonant (or `anomalous') X-ray diffraction spectra collected across the absorption K edge of Ti (4.966 keV) on a single Bragg reflection demonstrate a huge intensity ratio above and below the edge, providing a polar domain contrast of ∼270. This allows one to map the spatial domain distribution in a periodically inverted sample, with a resolution of ∼1 µm achieved with a microfocused beam. This non-contact, non-destructive technique is well suited for samples of large dimensions (in contrast with traditional resonant X-ray methods based on diffraction from Friedel pairs), and its potential is particularly relevant in the context of physical phenomena connected with an absence of inversion symmetry, which require characterization of the underlying absolute atomic structure (such as in the case of magnetoelectric coupling and multiferroics).text/htmlIdentification of inversion domains in KTiOPO4 via resonant X-ray diffractiontext4712015-05-14Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers361med@iucr.org3672053-2733Theoretical study of the properties of X-ray diffraction moiré fringes. I
http://scripts.iucr.org/cgi-bin/paper?td5025
A detailed and comprehensive theoretical description of X-ray diffraction moiré fringes for a bicrystal specimen is given on the basis of a calculation by plane-wave dynamical diffraction theory. Firstly, prior to discussing the main subject of the paper, a previous article [Yoshimura (1997). Acta Cryst. A53, 810–812] on the two-dimensionality of diffraction moiré patterns is restated on a thorough calculation of the moiré interference phase. Then, the properties of moiré fringes derived from the above theory are explained for the case of a plane-wave diffraction image, where the significant effect of Pendellösung intensity oscillation on the moiré pattern when the crystal is strained is described in detail with theoretically simulated moiré images. Although such plane-wave moiré images are not widely observed in a nearly pure form, knowledge of their properties is essential for the understanding of diffraction moiré fringes in general.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Yoshimura, J.2015-05-14doi:10.1107/S2053273315004970International Union of CrystallographyA detailed and comprehensive theoretical description of X-ray diffraction moiré fringes for a bicrystal specimen is given on the basis of a calculation by plane-wave dynamical diffraction theory, where the effect of the Pendellösung intensity oscillation on the moiré pattern is explained in detail.enDIFFRACTION MOIRE FRINGES; PENDELLOSUNG OSCILLATION; PHASE JUMP; GAP PHASEA detailed and comprehensive theoretical description of X-ray diffraction moiré fringes for a bicrystal specimen is given on the basis of a calculation by plane-wave dynamical diffraction theory. Firstly, prior to discussing the main subject of the paper, a previous article [Yoshimura (1997). Acta Cryst. A53, 810–812] on the two-dimensionality of diffraction moiré patterns is restated on a thorough calculation of the moiré interference phase. Then, the properties of moiré fringes derived from the above theory are explained for the case of a plane-wave diffraction image, where the significant effect of Pendellösung intensity oscillation on the moiré pattern when the crystal is strained is described in detail with theoretically simulated moiré images. Although such plane-wave moiré images are not widely observed in a nearly pure form, knowledge of their properties is essential for the understanding of diffraction moiré fringes in general.text/htmlTheoretical study of the properties of X-ray diffraction moiré fringes. Itext4712015-05-14Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers368med@iucr.org3812053-2733The revival of the Bravais lattice
http://scripts.iucr.org/cgi-bin/paper?me0569
The implications of the paper by Grimmer [Acta Cryst. (2015), A71, 143–149] are discussed.urn:issn:2053-2733Flack, H.D.2015-02-11doi:10.1107/S2053273315002557International Union of CrystallographyCrystallographers need to understand better the Bravais lattice.enBRAVAIS LATTICES; PHASE TRANSFORMATIONS; CELL REDUCTION; CRYSTALLOGRAPHIC NOMENCLATUREThe implications of the paper by Grimmer [Acta Cryst. (2015), A71, 143–149] are discussed.text/htmlThe revival of the Bravais latticetext2712015-02-11Acta Crystallographica Section A: Foundations and Advances2053-2733scientific commentaries141med@iucr.org1422053-2733X-ray investigation of lateral hetero-structures of inversion domains in LiNbO3, KTiOPO4 and KTiOAsO4
http://scripts.iucr.org/cgi-bin/paper?wo5016
In this paper periodically domain-inverted (PDI) ferroelectric crystals are studied using high-resolution X-ray diffraction. Rocking curves and reciprocal-space maps of the principal symmetric Bragg reflections in LiNbO3 (LN) (Λ = 5 µm), KTiOPO4 (KTP) (Λ = 9 µm) and KTiOAsO4 (KTA) (Λ = 39 µm) are presented. For all the samples strong satellite reflections were observed as a consequence of the PDI structure. Analysis of the satellites showed that they were caused by a combination of coherent and incoherent scattering between the adjacent domains. Whilst the satellites contained phase information regarding the structure of the domain wall, this information could not be rigorously extracted without a priori knowledge of the twinning mechanism. Analysis of the profiles reveals strain distributions of Δd/d = 1.6 × 10−4 and 2.0 × 10−4 perpendicular to domain walls in KTP and LN samples, respectively, and lateral correlation lengths of 63 µm (KTP), 194 µm (KTA) and 10 µm (LN). The decay of crystal truncation rods in LN and KTP was found to support the occurrence of surface corrugations.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Lyford, T.S.Collins, S.P.Fewster, P.F.Thomas, P.A.2015-03-13doi:10.1107/S2053273315001503International Union of CrystallographyPeriodically-poled ferroelectric crystals are studied by observing their superlattice (grating) diffraction profiles with high-resolution X-ray diffraction. In order to successfully model the data, the effects of strain, and sample and beam coherence, must be taken into account.enFERROELECTRICS; DIFFRACTION; COHERENCE; SYNCHROTRON RADIATION; GRATINGIn this paper periodically domain-inverted (PDI) ferroelectric crystals are studied using high-resolution X-ray diffraction. Rocking curves and reciprocal-space maps of the principal symmetric Bragg reflections in LiNbO3 (LN) (Λ = 5 µm), KTiOPO4 (KTP) (Λ = 9 µm) and KTiOAsO4 (KTA) (Λ = 39 µm) are presented. For all the samples strong satellite reflections were observed as a consequence of the PDI structure. Analysis of the satellites showed that they were caused by a combination of coherent and incoherent scattering between the adjacent domains. Whilst the satellites contained phase information regarding the structure of the domain wall, this information could not be rigorously extracted without a priori knowledge of the twinning mechanism. Analysis of the profiles reveals strain distributions of Δd/d = 1.6 × 10−4 and 2.0 × 10−4 perpendicular to domain walls in KTP and LN samples, respectively, and lateral correlation lengths of 63 µm (KTP), 194 µm (KTA) and 10 µm (LN). The decay of crystal truncation rods in LN and KTP was found to support the occurrence of surface corrugations.text/htmlX-ray investigation of lateral hetero-structures of inversion domains in LiNbO3, KTiOPO4 and KTiOAsO4text713http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2015-03-13255research papers2053-2733med@iucr.org2672053-2733Partial order among the 14 Bravais types of lattices: basics and applications
http://scripts.iucr.org/cgi-bin/paper?eo5044
Neither International Tables for Crystallography (ITC) nor available crystallography textbooks state explicitly which of the 14 Bravais types of lattices are special cases of others, although ITC contains the information necessary to derive the result in two ways, considering either the symmetry or metric properties of the lattices. The first approach is presented here for the first time, the second has been given by Michael Klemm in 1982. Metric relations between conventional bases of special and general lattice types are tabulated and applied to continuous equi-translation phase transitions.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Grimmer, H.2015-01-29doi:10.1107/S2053273314027351International Union of CrystallographyThe partial order among Bravais types of lattices obtained by considering special cases is derived from their space-group symmetry and applied to continuous equi-translation phase transitions.enBRAVAIS LATTICES; TRANSLATIONENGLEICHE SUBGROUPS; PHASE TRANSITIONSNeither International Tables for Crystallography (ITC) nor available crystallography textbooks state explicitly which of the 14 Bravais types of lattices are special cases of others, although ITC contains the information necessary to derive the result in two ways, considering either the symmetry or metric properties of the lattices. The first approach is presented here for the first time, the second has been given by Michael Klemm in 1982. Metric relations between conventional bases of special and general lattice types are tabulated and applied to continuous equi-translation phase transitions.text/htmlPartial order among the 14 Bravais types of lattices: basics and applicationstext2712015-01-29Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers143med@iucr.org1492053-2733Report of the Executive Committee for 2013
http://scripts.iucr.org/cgi-bin/paper?es0406
The report of the Executive Committee for 2013 is presented.urn:issn:2053-2733Dacombe, M.2015-01-01doi:10.1107/S2053273314015484International Union of CrystallographyThe report of the Executive Committee for 2013 is presented.enREPORT OF THE EXECUTIVE COMMITTEEThe report of the Executive Committee for 2013 is presented.text/htmlReport of the Executive Committee for 2013text1712015-01-01Acta Crystallographica Section A: Foundations and Advances2053-2733international union of crystallography114med@iucr.org1402053-2733Diffuse multiple scattering
http://scripts.iucr.org/cgi-bin/paper?td5022
A new form of diffraction lines has been identified, similar to Rutherford, Kikuchi and Kossel lines. This paper highlights some of the properties of these lines and shows how they can be used to eliminate the need for sample/source matching in Lonsdale's triple convergent line method in lattice-parameter determination.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Nisbet, A.G.A.Beutier, G.Fabrizi, F.Moser, B.Collins, S.P.2015-01-01doi:10.1107/S2053273314026515International Union of CrystallographyA new form of diffraction lines similar to Rutherford, Kikuchi and Kossel lines has been identified. They can be used to eliminate the need for sample/source matching in Lonsdale's triple convergent line method in lattice-parameter determination.enDIFFUSE SCATTERING; MULTIPLE SCATTERING; KOSSEL LINES; KIKUCHI LINES; STRAIN; LATTICE PARAMETERSA new form of diffraction lines has been identified, similar to Rutherford, Kikuchi and Kossel lines. This paper highlights some of the properties of these lines and shows how they can be used to eliminate the need for sample/source matching in Lonsdale's triple convergent line method in lattice-parameter determination.text/htmlDiffuse multiple scatteringtext1712015-01-01Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers20med@iucr.org252053-2733SHELXT – Integrated space-group and crystal-structure determination
http://scripts.iucr.org/cgi-bin/paper?sc5086
The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Sheldrick, G.M.2015-01-01doi:10.1107/S2053273314026370International Union of CrystallographySHELXT automates routine small-molecule structure determination starting from single-crystal reflection data, the Laue group and a reasonable guess as to which elements might be present.enPATTERSON SUPERPOSITION; DIRECT METHODS; DUAL-SPACE RECYCLING; SPACE-GROUP DETERMINATION; ELEMENT ASSIGNMENTThe new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.text/htmlSHELXT – Integrated space-group and crystal-structure determinationtext1712015-01-01Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers3med@iucr.org82053-2733Twenty-Third General Assembly and International Congress of Crystallography, Montreal, Canada, 5–12 August 2014
http://scripts.iucr.org/cgi-bin/paper?es0407
A report of the Twenty-Third General Assembly and International Congress of Crystallography is given.urn:issn:2053-2733IUCr2016-01-01doi:10.1107/S2053273314024425International Union of CrystallographyA report of the Twenty-Third General Assembly and International Congress of Crystallography is given.enINTERNATIONAL UNION OF CRYSTALLOGRAPHY; GENERAL ASSEMBLY; INTERNATIONAL CONGRESS OF CRYSTALLOGRAPHYA report of the Twenty-Third General Assembly and International Congress of Crystallography is given.text/htmlTwenty-Third General Assembly and International Congress of Crystallography, Montreal, Canada, 5–12 August 2014text1722016-01-01Acta Crystallographica Section A: Foundations and Advances2053-2733international union of crystallography85med@iucr.org1672053-2733New capabilities for `colouring in' the chemistry of crystal defects atom-by-atom
http://scripts.iucr.org/cgi-bin/paper?me0553
The latest generation of scanning transmission electron microscopes equipped with high-efficiency energy-dispersive X-ray detectors are breaking new ground with respect to high-resolution elemental imaging of materials. In this issue, Paulauskas et al. [Acta Cryst. (2014), A70, 524–531] demonstrate impressive results when applying this technique to improve understanding of CdTe dislocation structures.urn:issn:2053-2733Haigh, S.J.2014-10-29doi:10.1107/S2053273314023055International Union of CrystallographyThe latest generation of scanning transmission electron microscopes equipped with high-efficiency energy-dispersive X-ray detectors are breaking new ground with respect to high-resolution elemental imaging of materials. In this issue, Paulauskas et al. [Acta Cryst. (2014), A70, 524–531] demonstrate impressive results when applying this technique to improve understanding of CdTe dislocation structures.enSCANNING TRANSMISSION ELECTRON MICROSCOPY; X-RAY ENERGY-DISPERSIVE SPECTROSCOPY; SPECTRUM IMAGING; ELEMENTAL ANALYSIS; NANOPARTICLESThe latest generation of scanning transmission electron microscopes equipped with high-efficiency energy-dispersive X-ray detectors are breaking new ground with respect to high-resolution elemental imaging of materials. In this issue, Paulauskas et al. [Acta Cryst. (2014), A70, 524–531] demonstrate impressive results when applying this technique to improve understanding of CdTe dislocation structures.text/htmlNew capabilities for `colouring in' the chemistry of crystal defects atom-by-atomtext706Acta Crystallographica Section A: Foundations and Advances2014-10-29521scientific commentaries2053-2733med@iucr.org5232053-2733The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected
http://scripts.iucr.org/cgi-bin/paper?pc5043
This paper describes the mathematical basis for olex2.refine, the new refinement engine which is integrated within the Olex2 program. Precise and clear equations are provided for every computation performed by this engine, including structure factors and their derivatives, constraints, restraints and twinning; a general overview is also given of the different components of the engine and their relation to each other. A framework for adding multiple general constraints with dependencies on common physical parameters is described. Several new restraints on atomic displacement parameters are also presented.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Bourhis, L.J.Dolomanov, O.V.Gildea, R.J.Howard, J.A.K.Puschmann, H.2015-01-01doi:10.1107/S2053273314022207International Union of CrystallographyAn in-depth presentation is given of olex2.refine, the new refinement engine integrated in the Olex2 program.enSMALL MOLECULES; REFINEMENT; CONSTRAINTS; RESTRAINTS; LEAST SQUARES; OLEX2This paper describes the mathematical basis for olex2.refine, the new refinement engine which is integrated within the Olex2 program. Precise and clear equations are provided for every computation performed by this engine, including structure factors and their derivatives, constraints, restraints and twinning; a general overview is also given of the different components of the engine and their relation to each other. A framework for adding multiple general constraints with dependencies on common physical parameters is described. Several new restraints on atomic displacement parameters are also presented.text/htmlThe anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissectedtext1712015-01-01Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers59med@iucr.org752053-2733Effects of merohedric twinning on the diffraction pattern. Erratum and corrigenda
http://scripts.iucr.org/cgi-bin/paper?xo9015
A number of corrections are made to the article by Nespolo et al. [Acta Cryst. (2014), A70, 106–125].Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733Nespolo, M.Ferraris, G.Souvignier, B.2014-10-02doi:10.1107/S205327331402107XInternational Union of CrystallographyA number of corrections are made to the article by Nespolo et al. [Acta Cryst. (2014), A70, 106–125].enMEROHEDRIC TWINNING; REFLECTION CONDITIONS; DIFFRACTION SYMMETRYA number of corrections are made to the article by Nespolo et al. [Acta Cryst. (2014), A70, 106–125].text/htmlEffects of merohedric twinning on the diffraction pattern. Erratum and corrigendatext706Copyright (c) 2014 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2014-10-02683addenda and errata2053-2733med@iucr.org6842053-2733Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method
http://scripts.iucr.org/cgi-bin/paper?pc5042
A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Ramadhar, T.R.Zheng, S.-L.Chen, Y.-S.Clardy, J.2015-01-01doi:10.1107/S2053273314019573International Union of CrystallographyThis report describes complete practical guidelines and insights for the crystalline sponge method, which have been derived through the first use of synchrotron radiation on these systems, and includes a procedure for faster synthesis of the sponges. These guidelines will be applicable to crystal sponge data collected at synchrotrons or in-house facilities, and will allow researchers to obtain reliable high-quality data and construct chemically and physically sensible models for guest structural determination.enX-RAY CRYSTALLOGRAPHY; CRYSTALLINE SPONGE METHOD; METAL-ORGANIC FRAMEWORK; SINGLE-CRYSTAL-TO-SINGLE-CRYSTAL TRANSFORMATION; SYNCHROTRON RADIATIONA detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.text/htmlAnalysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge methodtext1712015-01-01Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers46med@iucr.org582053-2733Density functional calculations of polysynthetic Brazil twinning in α-quartz. Corrigenda and addenda
http://scripts.iucr.org/cgi-bin/paper?pc5044
Two corrections and a number of additions are made to the article by Grimmer & Delley [Acta Cryst. (2012), A68, 359–365].Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733Grimmer, H.Delley, B.2014-09-19doi:10.1107/S2053273314016842International Union of CrystallographyTwo corrections and a number of additions are made to the article by Grimmer & Delley [Acta Cryst. (2012), A68, 359–365].en[ALPHA]-QUARTZ; TWINNING; DENSITY FUNCTIONAL CALCULATIONSTwo corrections and a number of additions are made to the article by Grimmer & Delley [Acta Cryst. (2012), A68, 359–365].text/htmlDensity functional calculations of polysynthetic Brazil twinning in α-quartz. Corrigenda and addendatext706Copyright (c) 2014 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2014-09-19682addenda and errata2053-2733med@iucr.org6822053-2733High-flux ptychographic imaging using the new 55 µm-pixel detector `Lambda' based on the Medipix3 readout chip
http://scripts.iucr.org/cgi-bin/paper?mq5026
Suitable detection systems that are capable of recording high photon count rates with single-photon detection are instrumental for coherent X-ray imaging. The new single-photon-counting pixel detector `Lambda' has been tested in a ptychographic imaging experiment on solar-cell nanowires using Kirkpatrick–Baez-focused 13.8 keV X-rays. Taking advantage of the high count rate of the Lambda and dynamic range expansion by the semi-transparent central stop, a high-dynamic-range diffraction signal covering more than seven orders of magnitude has been recorded, which corresponds to a photon flux density of about 105 photons nm−2 s−1 or a flux of ∼1010 photons s−1 on the sample. By comparison with data taken without the semi-transparent central stop, an increase in resolution by a factor of 3–4 is determined: from about 125 nm to about 38 nm for the nanowire and from about 83 nm to about 21 nm for the illuminating wavefield.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Wilke, R.N.Wallentin, J.Osterhoff, M.Pennicard, D.Zozulya, A.Sprung, M.Salditt, T.2014-09-12doi:10.1107/S2053273314014545International Union of CrystallographyThe Large Area Medipix-Based Detector Array (Lambda) has been used in a ptychographic imaging experiment on solar-cell nanowires. By using a semi-transparent central stop, the high flux density provided by nano-focusing Kirkpatrick–Baez mirrors can be fully exploited for high-resolution phase reconstructions.enPHASE RETRIEVAL; PTYCHOGRAPHY; COHERENT DIFFRACTIVE IMAGING; SEMI-TRANSPARENT CENTRAL STOP; SEMI-TRANSPARENT BEAM STOP; LAMBDA DETECTOR; MEDIPIX3 CHIP; SOLAR-CELL NANOWIRESSuitable detection systems that are capable of recording high photon count rates with single-photon detection are instrumental for coherent X-ray imaging. The new single-photon-counting pixel detector `Lambda' has been tested in a ptychographic imaging experiment on solar-cell nanowires using Kirkpatrick–Baez-focused 13.8 keV X-rays. Taking advantage of the high count rate of the Lambda and dynamic range expansion by the semi-transparent central stop, a high-dynamic-range diffraction signal covering more than seven orders of magnitude has been recorded, which corresponds to a photon flux density of about 105 photons nm−2 s−1 or a flux of ∼1010 photons s−1 on the sample. By comparison with data taken without the semi-transparent central stop, an increase in resolution by a factor of 3–4 is determined: from about 125 nm to about 38 nm for the nanowire and from about 83 nm to about 21 nm for the illuminating wavefield.text/htmlHigh-flux ptychographic imaging using the new 55 µm-pixel detector `Lambda' based on the Medipix3 readout chiptext706http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2014-09-12research papers2053-2733med@iucr.org2053-2733Report of the Executive Committee for 2012
http://scripts.iucr.org/cgi-bin/paper?es0403
The report of the Executive Committee for 2012 is presented.urn:issn:2053-2733Dacombe, M.2014-06-11doi:10.1107/S2053273313022584International Union of CrystallographyThe report of the Executive Committee for 2012 is presented.enREPORT OF THE EXECUTIVE COMMITTEEThe report of the Executive Committee for 2012 is presented.text/htmlReport of the Executive Committee for 2012text704Acta Crystallographica Section A: Foundations and Advances2014-06-11385international union of crystallography2053-2733med@iucr.org4152053-2733Phasing in Crystallography: A Modern Perspective. By Carmelo Giacovazzo. IUCr Texts on Crystallography, No. 20. International Union of Crystallography/Oxford University Press, 2013. Pp. 432. Price GBP 65.00 (hardback). ISBN 978-0-19-968699-5.
http://scripts.iucr.org/cgi-bin/paper?xo0002
Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733Blessing, R.H.2014-07-17doi:10.1107/S2053273314010651International Union of CrystallographyenBOOK REVIEWtext/htmlPhasing in Crystallography: A Modern Perspective. By Carmelo Giacovazzo. IUCr Texts on Crystallography, No. 20. International Union of Crystallography/Oxford University Press, 2013. Pp. 432. Price GBP 65.00 (hardback). ISBN 978-0-19-968699-5.text5702014-07-17Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2014 International Union of Crystallography2053-2733book reviews518med@iucr.org5192053-2733On the temperature dependence of H-Uiso in the riding hydrogen model
http://scripts.iucr.org/cgi-bin/paper?kx5033
The temperature dependence of H-Uiso in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uiso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Lübben, J.Volkmann, C.Grabowsky, S.Edwards, A.Morgenroth, W.Fabbiani, F.P.A.Sheldrick, G.M.Dittrich, B.2014-05-28doi:10.1107/S2053273314010626International Union of CrystallographyThe temperature dependence of hydrogen Uiso and parent Ueq in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K.enRIDING HYDROGEN MODEL; QM/MM COMPUTATIONS; NEUTRON DIFFRACTION; INVARIOM REFINEMENT; HIRSHFELD-ATOM REFINEMENT; SYNCHROTRON RADIATIONThe temperature dependence of H-Uiso in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-Uiso below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for this study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.text/htmlOn the temperature dependence of H-Uiso in the riding hydrogen modeltext704http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations and Advances2014-05-28309research papers2053-2733med@iucr.org3162053-2733Notes for authors
http://scripts.iucr.org/cgi-bin/paper?me0517
urn:issn:2053-2733IUCr Editorial Office2014-05-02doi:10.1107/S2053273313022894International Union of CrystallographyNotes for authors.enNOTES FOR AUTHORStext/htmlNotes for authorstext3702014-05-02Acta Crystallographica Section A: Foundations and Advances2053-2733international union of crystallography303med@iucr.org3072053-2733On the subgroup structure of the hyperoctahedral group in six dimensions
http://scripts.iucr.org/cgi-bin/paper?eo5032
The subgroup structure of the hyperoctahedral group in six dimensions is investigated. In particular, the subgroups isomorphic to the icosahedral group are studied. The orthogonal crystallographic representations of the icosahedral group are classified and their intersections and subgroups analysed, using results from graph theory and their spectra.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Zappa, E.Dykeman, E.C.Twarock, R.2014-07-10doi:10.1107/S2053273314007712International Union of CrystallographyThe subgroup structure of the hyperoctahedral group in six dimensions is studied, with particular attention to the subgroups isomorphic to the icosahedral group. The orthogonal crystallographic representations of the icosahedral group are classified, and their intersections are studied in some detail, using a combinatorial approach which involves results from graph theory and their spectra.enSYMMETRY; CRYSTALLOGRAPHIC REPRESENTATION; ICOSAHEDRAL GROUP; HYPEROCTAHEDRAL GROUP; SPECTRAL GRAPH THEORYThe subgroup structure of the hyperoctahedral group in six dimensions is investigated. In particular, the subgroups isomorphic to the icosahedral group are studied. The orthogonal crystallographic representations of the icosahedral group are classified and their intersections and subgroups analysed, using results from graph theory and their spectra.text/htmlOn the subgroup structure of the hyperoctahedral group in six dimensionstext5702014-07-10Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papersmed@iucr.org2053-2733The wingspan of mathematical crystallography
http://scripts.iucr.org/cgi-bin/paper?me0541
The resurgence in mathematical crystallography motivated the formation of the IUCr Commission on Mathematical Crystallography, as well as this virtual special issue of Acta Crystallographica Section A. This foreword describes some of the current activities of the Commission and introduces the articles in the special issue.Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733Nespolo, M.McColm, G.2014-05-28doi:10.1107/S2053273314007463International Union of CrystallographyThe current activities of the IUCr Commission on Mathematical Crystallography are described and the articles in this virtual special issue on mathematical crystallography are introduced.enMATHEMATICAL CRYSTALLOGRAPHY; EDITORIALThe resurgence in mathematical crystallography motivated the formation of the IUCr Commission on Mathematical Crystallography, as well as this virtual special issue of Acta Crystallographica Section A. This foreword describes some of the current activities of the Commission and introduces the articles in the special issue.text/htmlThe wingspan of mathematical crystallographytext704Copyright (c) 2014 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2014-05-28317editorial2053-2733med@iucr.org3182053-2733A new theory for X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?sc5066
This article proposes a new theory of X-ray scattering that has particular relevance to powder diffraction. The underlying concept of this theory is that the scattering from a crystal or crystallite is distributed throughout space: this leads to the effect that enhanced scatter can be observed at the `Bragg position' even if the `Bragg condition' is not satisfied. The scatter from a single crystal or crystallite, in any fixed orientation, has the fascinating property of contributing simultaneously to many `Bragg positions'. It also explains why diffraction peaks are obtained from samples with very few crystallites, which cannot be explained with the conventional theory. The intensity ratios for an Si powder sample are predicted with greater accuracy and the temperature factors are more realistic. Another consequence is that this new theory predicts a reliability in the intensity measurements which agrees much more closely with experimental observations compared to conventional theory that is based on `Bragg-type' scatter. The role of dynamical effects (extinction etc.) is discussed and how they are suppressed with diffuse scattering. An alternative explanation for the Lorentz factor is presented that is more general and based on the capture volume in diffraction space. This theory, when applied to the scattering from powders, will evaluate the full scattering profile, including peak widths and the `background'. The theory should provide an increased understanding of the reliability of powder diffraction measurements, and may also have wider implications for the analysis of powder diffraction data, by increasing the accuracy of intensities predicted from structural models.http://creativecommons.org/licenses/by/2.0/ukurn:issn:2053-2733Fewster, P.F.2014-03-27doi:10.1107/S205327331400117XInternational Union of CrystallographyBy considering the scattering distributed throughout space, there is an intensity enhancement at the Bragg angle even when the Bragg condition is not satisfied. This leads to an alternative explanation for the diffraction from powders and small crystals.enDIFFRACTION THEORY; POWDER DIFFRACTION; SMALL CRYSTALSThis article proposes a new theory of X-ray scattering that has particular relevance to powder diffraction. The underlying concept of this theory is that the scattering from a crystal or crystallite is distributed throughout space: this leads to the effect that enhanced scatter can be observed at the `Bragg position' even if the `Bragg condition' is not satisfied. The scatter from a single crystal or crystallite, in any fixed orientation, has the fascinating property of contributing simultaneously to many `Bragg positions'. It also explains why diffraction peaks are obtained from samples with very few crystallites, which cannot be explained with the conventional theory. The intensity ratios for an Si powder sample are predicted with greater accuracy and the temperature factors are more realistic. Another consequence is that this new theory predicts a reliability in the intensity measurements which agrees much more closely with experimental observations compared to conventional theory that is based on `Bragg-type' scatter. The role of dynamical effects (extinction etc.) is discussed and how they are suppressed with diffuse scattering. An alternative explanation for the Lorentz factor is presented that is more general and based on the capture volume in diffraction space. This theory, when applied to the scattering from powders, will evaluate the full scattering profile, including peak widths and the `background'. The theory should provide an increased understanding of the reliability of powder diffraction measurements, and may also have wider implications for the analysis of powder diffraction data, by increasing the accuracy of intensities predicted from structural models.text/htmlA new theory for X-ray diffractiontext3702014-03-27Acta Crystallographica Section A: Foundations and Advanceshttp://creativecommons.org/licenses/by/2.0/uk2053-2733research papers257med@iucr.org2822053-2733Quasicrystals. A Primer, second edition. By Christian Janot. Oxford Classic Texts in the Physical Sciences. Oxford University Press, 2012. Pp. 427. Price GBP 42.50 (paperback). ISBN 978-0-19-965740-7.
http://scripts.iucr.org/cgi-bin/paper?pf0106
Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733de Boissieu, M.2014-05-02doi:10.1107/S2053273314000266International Union of CrystallographyenBOOK REVIEWtext/htmlQuasicrystals. A Primer, second edition. By Christian Janot. Oxford Classic Texts in the Physical Sciences. Oxford University Press, 2012. Pp. 427. Price GBP 42.50 (paperback). ISBN 978-0-19-965740-7.text3702014-05-02Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2014 International Union of Crystallography2053-2733book reviews308med@iucr.org3082053-2733Reflections on the magnetic pair distribution function
http://scripts.iucr.org/cgi-bin/paper?me0534
The recent application of the total scattering method to magnetic systems is discussed. The ability to determine the magnetic pair distribution function opens the door to the study of local order in magnetic systems ranging from multiferroics to dilute magnetic semiconductors.Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733Ratcliff, W.2013-12-20doi:10.1107/S2053273313033925International Union of CrystallographyThe recent application of the total scattering method to magnetic systems is discussed. The ability to determine the magnetic pair distribution function opens the door to the study of local order in magnetic systems ranging from multiferroics to dilute magnetic semiconductors.enMAGNETISM; TOTAL SCATTERING; NEUTRON SCATTERINGThe recent application of the total scattering method to magnetic systems is discussed. The ability to determine the magnetic pair distribution function opens the door to the study of local order in magnetic systems ranging from multiferroics to dilute magnetic semiconductors.text/htmlReflections on the magnetic pair distribution functiontext1702013-12-20Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2014 International Union of Crystallography2053-2733scientific commentaries1med@iucr.org22053-2733Essentials of Crystallography, second edition. By M. A. Wahab. Narosa Publishing House, 2014. Pp. xix + 335. Price USD 98.00 (North and South America), GBP 49.95 (rest of the World outside the Indian sub-continent). ISBN 978-1842658413 (outside the Indian sub-continent), 978-81-8487-316-0 (in the Indian sub-continent).
http://scripts.iucr.org/cgi-bin/paper?pf0116
Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733Nespolo, M.2014-02-20doi:10.1107/S2053273313032919International Union of CrystallographyenBOOK REVIEWtext/htmlEssentials of Crystallography, second edition. By M. A. Wahab. Narosa Publishing House, 2014. Pp. xix + 335. Price USD 98.00 (North and South America), GBP 49.95 (rest of the World outside the Indian sub-continent). ISBN 978-1842658413 (outside the Indian sub-continent), 978-81-8487-316-0 (in the Indian sub-continent).text2702014-02-20Acta Crystallographica Section A: Foundations and AdvancesCopyright (c) 2014 International Union of Crystallography2053-2733book reviews199med@iucr.org2022053-2733Early Days of X-ray Crystallography. By André Authier. International Union of Crystallography/Oxford University Press, 2013. Pp. xiv + 441. Price (hardcover) GBP 45.00. ISBN 978-0-19-965984-5.
http://scripts.iucr.org/cgi-bin/paper?pf0114
Copyright (c) 2014 International Union of Crystallographyurn:issn:2053-2733Helliwell, J.R.2013-11-23doi:10.1107/S2053273313027642International Union of CrystallographyenBOOK REVIEWtext/htmlEarly Days of X-ray Crystallography. By André Authier. International Union of Crystallography/Oxford University Press, 2013. Pp. xiv + 441. Price (hardcover) GBP 45.00. ISBN 978-0-19-965984-5.text701Copyright (c) 2014 International Union of CrystallographyActa Crystallographica Section A: Foundations and Advances2013-11-23book reviews2053-2733med@iucr.org2053-2733Incommensurate Crystallography. By Sander van Smaalen. IUCr Monographs on Crystallography, No. 21. Oxford University Press, 2012. Pp. 284. Price (paperback) GBP 37.50. ISBN 978-0-19-965923-4.
http://scripts.iucr.org/cgi-bin/paper?pf0110
Copyright (c) 2013 International Union of Crystallographyurn:issn:0108-7673Chapuis, G.2013-11-01doi:10.1107/S010876731301951XInternational Union of CrystallographyenBOOK REVIEWtext/htmlIncommensurate Crystallography. By Sander van Smaalen. IUCr Monographs on Crystallography, No. 21. Oxford University Press, 2012. Pp. 284. Price (paperback) GBP 37.50. ISBN 978-0-19-965923-4.text696Copyright (c) 2013 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2013-11-01620book reviews0108-7673med@iucr.org6211600-5724Semi-transparent central stop in high-resolution X-ray ptychography using Kirkpatrick–Baez focusing
http://scripts.iucr.org/cgi-bin/paper?mq5015
A ptychographic coherent X-ray diffractive imaging (PCDI) experiment has been carried out using 7.9 keV X-rays and Kirkpatrick–Baez focusing mirrors. By introducing a semi-transparent central stop in front of the detector the dynamic range on the detector is increased by about four orders of magnitude. The feasibility of this experimental scheme is demonstrated for PCDI applications with a resolution below 10 nm. The results are compared with reference data and an increase of resolution by a factor of two is obtained, while the deviation of the reconstructed phase map from the reference is below 1%.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Wilke, R.N.Vassholz, M.Salditt, T.2013-09-01doi:10.1107/S0108767313019612International Union of CrystallographyA semi-transparent central stop has been used for ptychographic coherent diffractive imaging to increase the effective dynamic range in the recording of the far-field diffraction patterns. In this way, the high flux density provided by nano-focusing Kirkpatrick–Baez mirrors can be fully exploited for high resolution and quantitative phase reconstructions.enPTYCHOGRAPHY; KIRKPATRICK-BAEZ MIRRORS; SEMI-TRANSPARENT CENTRAL STOP; SEMI-TRANSPARENT BEAM STOP; COHERENT DIFFRACTIVE IMAGING; PHASE RECONSTRUCTIONA ptychographic coherent X-ray diffractive imaging (PCDI) experiment has been carried out using 7.9 keV X-rays and Kirkpatrick–Baez focusing mirrors. By introducing a semi-transparent central stop in front of the detector the dynamic range on the detector is increased by about four orders of magnitude. The feasibility of this experimental scheme is demonstrated for PCDI applications with a resolution below 10 nm. The results are compared with reference data and an increase of resolution by a factor of two is obtained, while the deviation of the reconstructed phase map from the reference is below 1%.text/htmlSemi-transparent central stop in high-resolution X-ray ptychography using Kirkpatrick–Baez focusingtext695http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations of Crystallography2013-09-01490research papers0108-7673med@iucr.org4971600-5724Geometry of Crystallographic Groups. By Andrzej Szczepański. World Scientific, 2012. Pp. 208. Price (hardcover) GBP 51.00. ISBN 978-981-4412-25-4.
http://scripts.iucr.org/cgi-bin/paper?pf0111
Copyright (c) 2013 International Union of Crystallographyurn:issn:0108-7673McColm, G.2013-09-01doi:10.1107/S0108767313018825International Union of CrystallographyenBOOK REVIEWtext/htmlGeometry of Crystallographic Groups. By Andrzej Szczepański. World Scientific, 2012. Pp. 208. Price (hardcover) GBP 51.00. ISBN 978-981-4412-25-4.text695Copyright (c) 2013 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2013-09-01book reviews0108-7673med@iucr.org1600-5724Digital electron diffraction – seeing the whole picture
http://scripts.iucr.org/cgi-bin/paper?td5013
The advantages of convergent-beam electron diffraction for symmetry determination at the scale of a few nm are well known. In practice, the approach is often limited due to the restriction on the angular range of the electron beam imposed by the small Bragg angle for high-energy electron diffraction, i.e. a large convergence angle of the incident beam results in overlapping information in the diffraction pattern. Techniques have been generally available since the 1980s which overcome this restriction for individual diffracted beams, by making a compromise between illuminated area and beam convergence. Here a simple technique is described which overcomes all of these problems using computer control, giving electron diffraction data over a large angular range for many diffracted beams from the volume given by a focused electron beam (typically a few nm or less). The increase in the amount of information significantly improves the ease of interpretation and widens the applicability of the technique, particularly for thin materials or those with larger lattice parameters.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Beanland, R.Thomas, P.J.Woodward, D.I.Thomas, P.A.Roemer, R.A.2013-07-01doi:10.1107/S0108767313010143International Union of CrystallographyComputer control of beam tilt and image capture allows the collection of electron diffraction patterns over a large angular range, without any overlap in diffraction data and from a region limited only by the size of the electron beam. This results in a significant improvement in data volumes and ease of interpretation.enELECTRON DIFFRACTION; SYMMETRY DETERMINATION; CBED; LACBED; COMPUTER CONTROLThe advantages of convergent-beam electron diffraction for symmetry determination at the scale of a few nm are well known. In practice, the approach is often limited due to the restriction on the angular range of the electron beam imposed by the small Bragg angle for high-energy electron diffraction, i.e. a large convergence angle of the incident beam results in overlapping information in the diffraction pattern. Techniques have been generally available since the 1980s which overcome this restriction for individual diffracted beams, by making a compromise between illuminated area and beam convergence. Here a simple technique is described which overcomes all of these problems using computer control, giving electron diffraction data over a large angular range for many diffracted beams from the volume given by a focused electron beam (typically a few nm or less). The increase in the amount of information significantly improves the ease of interpretation and widens the applicability of the technique, particularly for thin materials or those with larger lattice parameters.text/htmlDigital electron diffraction – seeing the whole picturetext694http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations of Crystallography2013-07-01427research papers0108-7673med@iucr.org4341600-5724Crystallography – An Introduction, 3rd ed. By Walter Borchardt-Ott. Springer, 2012. Pp. xvi + 357. Price (paperback) EUR 42.75. ISBN 978-3-642-16451-4.
http://scripts.iucr.org/cgi-bin/paper?pf0109
Copyright (c) 2013 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2013-07-01doi:10.1107/S0108767313006624International Union of CrystallographyenBOOK REVIEWtext/htmlCrystallography – An Introduction, 3rd ed. By Walter Borchardt-Ott. Springer, 2012. Pp. xvi + 357. Price (paperback) EUR 42.75. ISBN 978-3-642-16451-4.text694Copyright (c) 2013 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2013-07-01457book reviews0108-7673med@iucr.org4581600-5724Report of the Executive Committee for 2011
http://scripts.iucr.org/cgi-bin/paper?es0397
The report of the Executive Committee for 2011 is presented.urn:issn:0108-7673Dacombe, M.2013-03-01doi:10.1107/S010876731202819XInternational Union of CrystallographyThe report of the Executive Committee for 2011 is presented.enREPORT OF THE EXECUTIVE COMMITTEEThe report of the Executive Committee for 2011 is presented.text/htmlReport of the Executive Committee for 2011text2692013-03-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673international union of crystallography210med@iucr.org2391600-5724Evolution of diffraction methods for solving crystal structures
http://scripts.iucr.org/cgi-bin/paper?wl0020
The discovery of X-ray diffraction in 1912 by Laue and co-workers had important implications for the physics of diffraction, for the nature of X-radiation and for the structure of matter. Lawrence Bragg made important contributions to early developments in each of these areas, but the most pregnant of his innovations was in structure determination from X-ray diffraction data. He continued to make highly significant contributions to structure determination right on to the first crystal structures of proteins. Crystallography has made substantial contributions to chemistry and biology, and notably so for biological macromolecules.urn:issn:0108-7673Hendrickson, W.A.2013-01-01doi:10.1107/S0108767312050453International Union of CrystallographyThe practices for determining the atomic structures in crystals have changed greatly over the century since Lawrence Bragg introduced the trial-and-error method by which he solved structures for rocksalt, iron pyrite and other salts and minerals. Structure determinations for biological macromolecules first borrowed from the small-molecule tradition that evolved, notably adopting isomorphous replacement; subsequently, however, new approaches have grown to dominate, notably anomalous diffraction and molecular replacement.enW. L. BRAGG; PHASING; STRUCTURE DETERMINATIONThe discovery of X-ray diffraction in 1912 by Laue and co-workers had important implications for the physics of diffraction, for the nature of X-radiation and for the structure of matter. Lawrence Bragg made important contributions to early developments in each of these areas, but the most pregnant of his innovations was in structure determination from X-ray diffraction data. He continued to make highly significant contributions to structure determination right on to the first crystal structures of proteins. Crystallography has made substantial contributions to chemistry and biology, and notably so for biological macromolecules.text/htmlEvolution of diffraction methods for solving crystal structurestext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673research papers51med@iucr.org591600-5724Early days in drug discovery by crystallography – personal recollections
http://scripts.iucr.org/cgi-bin/paper?wl0019
The influences of Lawrence Bragg and Max Perutz are evident in the contemporary emphasis on `structural enablement' in drug discovery. On this occasion of the centenary of Bragg's equation, his role in supporting the earliest structural studies of biological materials at the Cavendish Laboratory is remembered. The 1962 Nobel Prizes for the structures of DNA and proteins marked the golden anniversary of the von Laue and Bragg discoveries.urn:issn:0108-7673Colman, P.M.2013-01-01doi:10.1107/S0108767312050441International Union of CrystallographyThe neuraminidase inhibitors for treatment of influenza are an early example of drug discovery by crystallography.enINFLUENZA; MEDICINE; NON-CRYSTALLOGRAPHIC SYMMETRYThe influences of Lawrence Bragg and Max Perutz are evident in the contemporary emphasis on `structural enablement' in drug discovery. On this occasion of the centenary of Bragg's equation, his role in supporting the earliest structural studies of biological materials at the Cavendish Laboratory is remembered. The 1962 Nobel Prizes for the structures of DNA and proteins marked the golden anniversary of the von Laue and Bragg discoveries.text/htmlEarly days in drug discovery by crystallography – personal recollectionstext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673research papers60med@iucr.org621600-5724Understanding Single-Crystal X-ray Crystallography. By Dennis W. Bennett. Weinheim: Wiley-VCH, 2010. Pp. xx + 811. Price (hardcover) GBP 115.00, EUR 138.00. ISBN 978-3-527-32677-8.
http://scripts.iucr.org/cgi-bin/paper?pf0103
Copyright (c) 2013 International Union of Crystallographyurn:issn:0108-7673Lecomte, C.2013-03-01doi:10.1107/S0108767313000639International Union of CrystallographyenBOOK REVIEWtext/htmlUnderstanding Single-Crystal X-ray Crystallography. By Dennis W. Bennett. Weinheim: Wiley-VCH, 2010. Pp. xx + 811. Price (hardcover) GBP 115.00, EUR 138.00. ISBN 978-3-527-32677-8.text2692013-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2013 International Union of Crystallography0108-7673book reviews208med@iucr.org2091600-5724Fifty years of aperiodic crystals. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?me0490
Corrections to the article by Janssen [Acta Cryst. (2012). A68, 667–674] are given.Copyright (c) 2013 International Union of Crystallographyurn:issn:0108-7673Janssen, T.2013-03-01doi:10.1107/S0108767313000238International Union of CrystallographyCorrigendum to the article by Janssen [Acta Cryst. (2012). A68, 667–674].enAPERIODICITY; QUASICRYSTALS; INCOMMENSURATE PHASESCorrections to the article by Janssen [Acta Cryst. (2012). A68, 667–674] are given.text/htmlFifty years of aperiodic crystals. Corrigendumtext2692013-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2013 International Union of Crystallography0108-7673addenda and erratamed@iucr.org1600-5724The significance of Bragg's law in electron diffraction and microscopy, and Bragg's second law
http://scripts.iucr.org/cgi-bin/paper?wl5169
Bragg's second law, which deserves to be more widely known, is recounted. The significance of Bragg's law in electron diffraction and microscopy is then discussed, with particular emphasis on differences between X-ray and electron diffraction. As an example of such differences, the critical voltage effect in electron diffraction is described. It is then shown that the lattice imaging of crystals in high-resolution electron microscopy directly reveals the Bragg planes used for the imaging process, exactly as visualized by Bragg in his real-space law. Finally, it is shown how in 2012, for the first time, on the centennial anniversary of Bragg's law, single atoms have been identified in an electron microscope using X-rays emitted from the specimen. Hence atomic resolution X-ray maps of a crystal in real space can be formed which give the positions and identities of the different atoms in the crystal, or of a single impurity atom in the crystal.urn:issn:0108-7673Humphreys, C.J.2013-01-01doi:10.1107/S0108767312047587International Union of CrystallographyThe significance of Bragg's law in electron diffraction is discussed, with particular emphasis on the differences between X-ray and electron diffraction. Recent developments in X-ray instrumentation in electron microscopy which enable single atoms to be imaged and identified using X-ray analysis within an electron microscope are described.enW. L. BRAGG; CRITICAL VOLTAGE EFFECT; ATOMIC RESOLUTION IMAGING; X-RAY MAPSBragg's second law, which deserves to be more widely known, is recounted. The significance of Bragg's law in electron diffraction and microscopy is then discussed, with particular emphasis on differences between X-ray and electron diffraction. As an example of such differences, the critical voltage effect in electron diffraction is described. It is then shown that the lattice imaging of crystals in high-resolution electron microscopy directly reveals the Bragg planes used for the imaging process, exactly as visualized by Bragg in his real-space law. Finally, it is shown how in 2012, for the first time, on the centennial anniversary of Bragg's law, single atoms have been identified in an electron microscope using X-rays emitted from the specimen. Hence atomic resolution X-ray maps of a crystal in real space can be formed which give the positions and identities of the different atoms in the crystal, or of a single impurity atom in the crystal.text/htmlThe significance of Bragg's law in electron diffraction and microscopy, and Bragg's second lawtext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673research papers45med@iucr.org501600-5724Lawrence Bragg, microdiffraction and X-ray lasers
http://scripts.iucr.org/cgi-bin/paper?wl5167
We trace the historical development of W. L. Bragg's `law' and the key experimental observation which made it possible using polychromatic radiation at a time when neither X-ray wavelengths nor cell constants were known. This led, through his phasing and solving large mineral structures (without use of a computer), to work on metals, proteins, bubble rafts and his X-ray microscope. The relationship of this to early X-ray microdiffraction is outlined, followed by a brief review of electron microdiffraction methods, where electron-probe sizes smaller than one unit cell can be formed with an interesting `failure' of Bragg's law. We end with a review of recent femtosecond X-ray `snapshot' diffraction from protein nanocrystals, using an X-ray laser which generates pulses so short that they terminate before radiation damage can commence, yet subsequently destroy the sample. In this way, using short pulses instead of freezing, the nexus between dose, resolution and crystal size has been broken, opening the way to time-resolved diffraction without damage for a stream of identical particles.urn:issn:0108-7673Spence, J.C.H.2013-01-01doi:10.1107/S0108767312046296International Union of CrystallographyThe history of Bragg's law, life and work is reviewed with particular reference to the development of X-ray and electron microdiffraction. A summary of recent work applying the hard X-ray free-electron laser to problems in structural biology is given.enBRAGG'S LAW; MICRODIFFRACTION; CONVERGENT-BEAM ELECTRON DIFFRACTION; CBED; X-RAY LASERS; TIME-RESOLVED DIFFRACTIONWe trace the historical development of W. L. Bragg's `law' and the key experimental observation which made it possible using polychromatic radiation at a time when neither X-ray wavelengths nor cell constants were known. This led, through his phasing and solving large mineral structures (without use of a computer), to work on metals, proteins, bubble rafts and his X-ray microscope. The relationship of this to early X-ray microdiffraction is outlined, followed by a brief review of electron microdiffraction methods, where electron-probe sizes smaller than one unit cell can be formed with an interesting `failure' of Bragg's law. We end with a review of recent femtosecond X-ray `snapshot' diffraction from protein nanocrystals, using an X-ray laser which generates pulses so short that they terminate before radiation damage can commence, yet subsequently destroy the sample. In this way, using short pulses instead of freezing, the nexus between dose, resolution and crystal size has been broken, opening the way to time-resolved diffraction without damage for a stream of identical particles.text/htmlLawrence Bragg, microdiffraction and X-ray laserstext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673research papers25med@iucr.org331600-5724The Bragg legacy: early days in macromolecular crystallography
http://scripts.iucr.org/cgi-bin/paper?wl5170
W. H. Bragg arrived in Australia in 1886 as Head of the Mathematics and Physics Departments at the University of Adelaide. His son, W. L. Bragg, grew up in Adelaide and graduated from the Physics Department. Many years later I graduated from the same department and had the opportunity to share Lawrence Bragg's recollections of life in Adelaide. As well as touching on the `Adelaide' connection, this report briefly reviews Bragg's critical role in encouraging, supporting and establishing the field of large-molecule crystallography.urn:issn:0108-7673Matthews, B.W.2013-01-01doi:10.1107/S0108767312042924International Union of CrystallographyW. L. Bragg's critical role in encouraging, supporting and establishing the field of large-molecule crystallography is reviewed.enADELAIDE; MAX PERUTZ; DOROTHY HODGKIN; HEN EGG-WHITE LYSOZYMEW. H. Bragg arrived in Australia in 1886 as Head of the Mathematics and Physics Departments at the University of Adelaide. His son, W. L. Bragg, grew up in Adelaide and graduated from the Physics Department. Many years later I graduated from the same department and had the opportunity to share Lawrence Bragg's recollections of life in Adelaide. As well as touching on the `Adelaide' connection, this report briefly reviews Bragg's critical role in encouraging, supporting and establishing the field of large-molecule crystallography.text/htmlThe Bragg legacy: early days in macromolecular crystallographytext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673research papers34med@iucr.org361600-5724Equivalence of superspace groups
http://scripts.iucr.org/cgi-bin/paper?pc5018
An algorithm is presented which determines the equivalence of two settings of a (3 + d)-dimensional superspace group (d = 1, 2, 3). The algorithm has been implemented as a web tool {\tt findssg} on {\tt SSG(3+d)D}, providing the transformation of any user-given superspace group to the standard setting of this superspace group in {\tt SSG(3+d)D}. It is shown how the standard setting of a superspace group can be directly obtained by an appropriate transformation of the external-space lattice vectors (the basic structure unit cell) and a transformation of the internal-space lattice vectors (new modulation wavevectors are linear combinations of old modulation wavevectors plus a three-dimensional reciprocal-lattice vector). The need for non-standard settings in some cases and the desirability of employing standard settings of superspace groups in other cases are illustrated by an analysis of the symmetries of a series of compounds, comparing published and standard settings and the transformations between them. A compilation is provided of standard settings of compounds with two- and three-dimensional modulations. The problem of settings of superspace groups is discussed for incommensurate composite crystals and for chiral superspace groups.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673van Smaalen, S.Campbell, B.J.Stokes, H.T.2013-01-01doi:10.1107/S0108767312041657International Union of CrystallographyThe standard settings of (3 + d)-dimensional superspace groups are determined for a series of modulated compounds, especially concentrating on d = 2 and 3. The coordinate transformation in superspace is discussed in view of its implications in physical space.enSYMMETRY; SUPERSPACE GROUPS; TWO-DIMENSIONALLY MODULATED CRYSTALS; THREE-DIMENSIONALLY MODULATED CRYSTALSAn algorithm is presented which determines the equivalence of two settings of a (3 + d)-dimensional superspace group (d = 1, 2, 3). The algorithm has been implemented as a web tool {\tt findssg} on {\tt SSG(3+d)D}, providing the transformation of any user-given superspace group to the standard setting of this superspace group in {\tt SSG(3+d)D}. It is shown how the standard setting of a superspace group can be directly obtained by an appropriate transformation of the external-space lattice vectors (the basic structure unit cell) and a transformation of the internal-space lattice vectors (new modulation wavevectors are linear combinations of old modulation wavevectors plus a three-dimensional reciprocal-lattice vector). The need for non-standard settings in some cases and the desirability of employing standard settings of superspace groups in other cases are illustrated by an analysis of the symmetries of a series of compounds, comparing published and standard settings and the transformations between them. A compilation is provided of standard settings of compounds with two- and three-dimensional modulations. The problem of settings of superspace groups is discussed for incommensurate composite crystals and for chiral superspace groups.text/htmlEquivalence of superspace groupstext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papers75med@iucr.org901600-5724A probabilistic approach to space-group determination from powder diffraction data. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?me0478
The name of the third author and an error in equation (9) of the article by Markvardsen et al. [Acta Cryst. (2001). A57, 47–54] are corrected.Copyright (c) 2012 International Union of Crystallographyurn:issn:0108-7673Markvardsen, A.J.David, W.I.F.Johnston, J.C.Shankland, K.2012-11-01doi:10.1107/S0108767312038305International Union of CrystallographyCorrigendum to the article by Markvardsen et al. [Acta Cryst. (2001). A57, 47–54].enPOWDER DIFFRACTIONThe name of the third author and an error in equation (9) of the article by Markvardsen et al. [Acta Cryst. (2001). A57, 47–54] are corrected.text/htmlA probabilistic approach to space-group determination from powder diffraction data. Corrigendumtext686Copyright (c) 2012 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2012-11-01780addenda and errata0108-7673med@iucr.org7801600-5724Fundamentals of X-ray Crystallography, second edition. By Dongcai Liang. Beijing: Science Press/Oxford: Alpha Science International Ltd, 2011. Pp. xi + 435. Price GBP 49.99. ISBN 978-1-84265-571-9.
http://scripts.iucr.org/cgi-bin/paper?pf0104
Copyright (c) 2012 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2012-11-01doi:10.1107/S0108767312037099International Union of CrystallographyenBOOK REVIEWtext/htmlFundamentals of X-ray Crystallography, second edition. By Dongcai Liang. Beijing: Science Press/Oxford: Alpha Science International Ltd, 2011. Pp. xi + 435. Price GBP 49.99. ISBN 978-1-84265-571-9.text686Copyright (c) 2012 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2012-11-01781book reviews0108-7673med@iucr.org7841600-5724The early development of neutron diffraction: science in the wings of the Manhattan Project
http://scripts.iucr.org/cgi-bin/paper?wl5168
Although neutron diffraction was first observed using radioactive decay sources shortly after the discovery of the neutron, it was only with the availability of higher intensity neutron beams from the first nuclear reactors, constructed as part of the Manhattan Project, that systematic investigation of Bragg scattering became possible. Remarkably, at a time when the war effort was singularly focused on the development of the atomic bomb, groups working at Oak Ridge and Chicago carried out key measurements and recognized the future utility of neutron diffraction quite independent of its contributions to the measurement of nuclear cross sections. Ernest O. Wollan, Lyle B. Borst and Walter H. Zinn were all able to observe neutron diffraction in 1944 using the X-10 graphite reactor and the CP-3 heavy water reactor. Subsequent work by Wollan and Clifford G. Shull, who joined Wollan's group at Oak Ridge in 1946, laid the foundations for widespread application of neutron diffraction as an important research tool.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Mason, T.E.Gawne, T.J.Nagler, S.E.Nestor, M.B.Carpenter, J.M.2013-01-01doi:10.1107/S0108767312036021International Union of CrystallographyEarly neutron diffraction experiments performed in 1944 using the first nuclear reactors are described.enNEUTRON DIFFRACTION; MANHATTAN PROJECTAlthough neutron diffraction was first observed using radioactive decay sources shortly after the discovery of the neutron, it was only with the availability of higher intensity neutron beams from the first nuclear reactors, constructed as part of the Manhattan Project, that systematic investigation of Bragg scattering became possible. Remarkably, at a time when the war effort was singularly focused on the development of the atomic bomb, groups working at Oak Ridge and Chicago carried out key measurements and recognized the future utility of neutron diffraction quite independent of its contributions to the measurement of nuclear cross sections. Ernest O. Wollan, Lyle B. Borst and Walter H. Zinn were all able to observe neutron diffraction in 1944 using the X-10 graphite reactor and the CP-3 heavy water reactor. Subsequent work by Wollan and Clifford G. Shull, who joined Wollan's group at Oak Ridge in 1946, laid the foundations for widespread application of neutron diffraction as an important research tool.text/htmlThe early development of neutron diffraction: science in the wings of the Manhattan Projecttext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papers37med@iucr.org441600-5724Lawrence Bragg's interest in the deformation of metals and 1950–1953 in the Cavendish – a worm's-eye view
http://scripts.iucr.org/cgi-bin/paper?wl5165
This paper recounts the atmosphere in the Cavendish Laboratory during Lawrence Bragg's triumphant final years there through the eyes and the work of a young research student, and hence reflects some measure of Bragg's personality. The opportunity is taken to deal in detail with Bragg's contribution to our understanding of crystal plasticity, which is seldom described, being overshadowed by his many superb contributions to the determination of crystal structure. Bragg produced in 1940–1942, through his development of the bubble model of a crystal structure, the first demonstration of how crystal dislocations move. His suggestion of the use of microbeams led rather directly to the development of modern thin-film transmission electron microscopy.urn:issn:0108-7673Kelly, A.2013-01-01doi:10.1107/S0108767312034356International Union of CrystallographyA research student's view of life in W. L. Bragg's Cavendish Laboratory from 1950–1953 is given. The use of the bubble raft in illustrating the properties of dislocations in crystals is described.enBUBBLES; DISLOCATIONS; MICROBEAMS; THIN-FILM MICROSCOPYThis paper recounts the atmosphere in the Cavendish Laboratory during Lawrence Bragg's triumphant final years there through the eyes and the work of a young research student, and hence reflects some measure of Bragg's personality. The opportunity is taken to deal in detail with Bragg's contribution to our understanding of crystal plasticity, which is seldom described, being overshadowed by his many superb contributions to the determination of crystal structure. Bragg produced in 1940–1942, through his development of the bubble model of a crystal structure, the first demonstration of how crystal dislocations move. His suggestion of the use of microbeams led rather directly to the development of modern thin-film transmission electron microscopy.text/htmlLawrence Bragg's interest in the deformation of metals and 1950–1953 in the Cavendish – a worm's-eye viewtext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673research papers16med@iucr.org241600-5724Fifty years of aperiodic crystals
http://scripts.iucr.org/cgi-bin/paper?wx5020
Historians often have debates about the beginning and end of a certain era. The same discussion can be had about the history of aperiodic crystals. There are reasons to claim that in 2012 one may celebrate the 50th anniversary of this field. A short description is given of the development of this branch of crystallography. It is argued that the most important point in its history is the discovery of quasicrystals, which has been recognized by awarding the Nobel Prize in Chemistry 2011 to Dan Shechtman.Copyright (c) 2012 International Union of Crystallographyurn:issn:0108-7673Janssen, T.2012-11-01doi:10.1107/S0108767312033715International Union of CrystallographyIn the 1960s the first examples were found of crystals which were not lattice periodic but quasiperiodic (a more general notion), contradicting the prevailing idea that crystals should be lattice periodic. The most interesting class of these aperiodic crystals was that of quasicrystals, discovered in 1982 by Dan Shechtman. A brief history of the development of the field of aperiodic crystals is given.enAPERIODICITY; QUASICRYSTALS; INCOMMENSURATE PHASESHistorians often have debates about the beginning and end of a certain era. The same discussion can be had about the history of aperiodic crystals. There are reasons to claim that in 2012 one may celebrate the 50th anniversary of this field. A short description is given of the development of this branch of crystallography. It is argued that the most important point in its history is the discovery of quasicrystals, which has been recognized by awarding the Nobel Prize in Chemistry 2011 to Dan Shechtman.text/htmlFifty years of aperiodic crystalstext686Copyright (c) 2012 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2012-11-01667feature articles0108-7673med@iucr.org6741600-5724Introduction to the Theory of Thermal Neutron Scattering, third edition. By G. L. Squires. Cambridge University Press, 2012. Pp. 270. Price (paperback) GBP 45.00. ISBN 978-1-107-64406-9.
http://scripts.iucr.org/cgi-bin/paper?pf0101
Copyright (c) 2012 International Union of Crystallographyurn:issn:0108-7673Braden, M.2012-09-01doi:10.1107/S0108767312031406International Union of CrystallographyenBOOK REVIEWtext/htmlIntroduction to the Theory of Thermal Neutron Scattering, third edition. By G. L. Squires. Cambridge University Press, 2012. Pp. 270. Price (paperback) GBP 45.00. ISBN 978-1-107-64406-9.text685Copyright (c) 2012 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2012-09-01665book reviews0108-7673med@iucr.org6651600-5724Background to the Nobel Prize to the Braggs
http://scripts.iucr.org/cgi-bin/paper?wl5166
The Nobel Committees have to follow the nominations submitted for a specific year. During the early phase of X-ray crystallography, a limited number of scientists were active. In 1914 Max von Laue and William Henry Bragg were both nominated and could have been awarded a joint Nobel Prize. However, a member of the Nobel Committee for Physics, Allvar Gullstrand, was well aware of the activities in the field and strongly recommended that only von Laue should receive the prize since a main contributor, William Laurence Bragg, was not nominated. Next year, when the First World War had started, there were few nominations, but now both Braggs, father and son, were nominated. Gullstrand was very pleased and recommended them both for the 1915 Nobel Prize in Physics. The rest of the committee agreed and this then became the decision of the Royal Academy for Sciences, Stockholm.urn:issn:0108-7673Liljas, A.2013-01-01doi:10.1107/S0108767312031133International Union of CrystallographyW. L. Bragg would have missed the Nobel Prize if his father had been awarded the prize together with von Laue in 1914. Fortunately, the Nobel Committee for Physics was aware of his contributions and decided to award the prize to W. H. Bragg together with his son in 1915, when they were both nominated.enNOBEL PRIZE; WILLIAM HENRY BRAGG; WILLIAM LAWRENCE BRAGG; X-RAY DIFFRACTION; ALLVAR GULLSTRAND; FIRST WORLD WARThe Nobel Committees have to follow the nominations submitted for a specific year. During the early phase of X-ray crystallography, a limited number of scientists were active. In 1914 Max von Laue and William Henry Bragg were both nominated and could have been awarded a joint Nobel Prize. However, a member of the Nobel Committee for Physics, Allvar Gullstrand, was well aware of the activities in the field and strongly recommended that only von Laue should receive the prize since a main contributor, William Laurence Bragg, was not nominated. Next year, when the First World War had started, there were few nominations, but now both Braggs, father and son, were nominated. Gullstrand was very pleased and recommended them both for the 1915 Nobel Prize in Physics. The rest of the committee agreed and this then became the decision of the Royal Academy for Sciences, Stockholm.text/htmlBackground to the Nobel Prize to the Braggstext1692013-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673research papers10med@iucr.org151600-5724Twenty-Second General Assembly and International Congress of Crystallography, Madrid, Spain, 22–30 August 2011
http://scripts.iucr.org/cgi-bin/paper?es0389
A report of the Twenty-Second General Assembly and International Congress of Crystallography is given.urn:issn:0108-7673IUCr2012-09-01doi:10.1107/S010876731200414XInternational Union of CrystallographyA report of the Twenty-Second General Assembly and International Congress of Crystallography is given.enA report of the Twenty-Second General Assembly and International Congress of Crystallography is given.text/htmlTwenty-Second General Assembly and International Congress of Crystallography, Madrid, Spain, 22–30 August 2011text685Acta Crystallographica Section A: Foundations of Crystallography2012-09-01607international union of crystallography0108-7673med@iucr.org6641600-5724Structure of Materials. An Introduction to Crystallography, Diffraction and Symmetry. By Marc De Graef and Michael E. McHenry. Pp. xxxi+844. Cambridge: Cambridge University Press. 3rd printing, 2010. Price (hardback) USD 118.00. ISBN: 978-0521651516.
http://scripts.iucr.org/cgi-bin/paper?pf0097
Copyright (c) 2012 International Union of Crystallographyurn:issn:0108-7673Paufler, P.2012-07-01doi:10.1107/S0108767312016534International Union of CrystallographyenBOOK RECEIVEDtext/htmlStructure of Materials. An Introduction to Crystallography, Diffraction and Symmetry. By Marc De Graef and Michael E. McHenry. Pp. xxxi+844. Cambridge: Cambridge University Press. 3rd printing, 2010. Price (hardback) USD 118.00. ISBN: 978-0521651516.text4682012-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2012 International Union of Crystallography0108-7673books received523med@iucr.org5231600-5724Enhanced rigid-bond restraints
http://scripts.iucr.org/cgi-bin/paper?pc5011
The rigid-bond model [Hirshfeld (1976). Acta Cryst. A32, 239–244] states that the mean-square displacements of two atoms are equal in the direction of the bond joining them. This criterion is widely used for verification (as intended by Hirshfeld) and also as a restraint in structure refinement as suggested by Rollett [Crystallographic Computing (1970), edited by F. R. Ahmed et al., pp. 167–181. Copenhagen: Munksgaard]. By reformulating this condition, so that the relative motion of the two atoms is required to be perpendicular to the bond, the number of restraints that can be applied per anisotropic atom is increased from about one to about three. Application of this condition to 1,3-distances in addition to the 1,2-distances means that on average just over six restraints can be applied to the six anisotropic displacement parameters of each atom. This concept is tested against very high resolution data of a small peptide and employed as a restraint for protein refinement at more modest resolution (e.g. 1.7 Å).http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Thorn, A.Dittrich, B.Sheldrick, G.M.2012-07-01doi:10.1107/S0108767312014535International Union of CrystallographyAn extension is proposed to the rigid-bond description of atomic thermal motion in crystals.enRIGID-BOND TEST; REFINEMENT RESTRAINTS; ANISOTROPIC DISPLACEMENT PARAMETERSThe rigid-bond model [Hirshfeld (1976). Acta Cryst. A32, 239–244] states that the mean-square displacements of two atoms are equal in the direction of the bond joining them. This criterion is widely used for verification (as intended by Hirshfeld) and also as a restraint in structure refinement as suggested by Rollett [Crystallographic Computing (1970), edited by F. R. Ahmed et al., pp. 167–181. Copenhagen: Munksgaard]. By reformulating this condition, so that the relative motion of the two atoms is required to be perpendicular to the bond, the number of restraints that can be applied per anisotropic atom is increased from about one to about three. Application of this condition to 1,3-distances in addition to the 1,2-distances means that on average just over six restraints can be applied to the six anisotropic displacement parameters of each atom. This concept is tested against very high resolution data of a small peptide and employed as a restraint for protein refinement at more modest resolution (e.g. 1.7 Å).text/htmlEnhanced rigid-bond restraintstext4682012-07-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papersmed@iucr.org1600-5724Basic Elements of Crystallography. By Nevill Gonzalez Szwacki and Teresa Szwacka. Pan Stanford Publishing, 2010. Pp. xi + 195. Price (paperback) GBP 49.99. ISBN 978-981-4241-59-5.
http://scripts.iucr.org/cgi-bin/paper?pf0093
Copyright (c) 2012 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2012-05-01doi:10.1107/S0108767312011968International Union of CrystallographyenBOOK REVIEWtext/htmlBasic Elements of Crystallography. By Nevill Gonzalez Szwacki and Teresa Szwacka. Pan Stanford Publishing, 2010. Pp. xi + 195. Price (paperback) GBP 49.99. ISBN 978-981-4241-59-5.text3682012-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2012 International Union of Crystallography0108-7673book reviews430med@iucr.org4321600-5724Report of the Executive Committee for 2010
http://scripts.iucr.org/cgi-bin/paper?es0388
The report of the Executive Committee for 2010 is presented.urn:issn:0108-7673Dacombe, M.2012-05-01doi:10.1107/S0108767311031370International Union of CrystallographyThe report of the Executive Committee for 2010 is presented.enREPORT OF THE EXECUTIVE COMMITTEEThe report of the Executive Committee for 2010 is presented.text/htmlReport of the Executive Committee for 2010text3682012-05-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673international union of crystallographymed@iucr.org1600-5724Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noise
http://scripts.iucr.org/cgi-bin/paper?cc5011
A new two-step algorithm is developed for reconstructing the three-dimensional diffraction intensity of a globular biological macromolecule from many experimentally measured quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The first step is classification of the two-dimensional patterns into groups according to the similarity of direction of the incident X-rays with respect to the molecule and an averaging within each group to reduce the noise. The second step is detection of common intersecting circles between the signal-enhanced two-dimensional patterns to identify their mutual location in the three-dimensional wavenumber space. The newly developed algorithm enables one to detect a signal for classification in noisy experimental photon-count data with as low as ∼0.1 photons per effective pixel. The wavenumber of such a limiting pixel determines the attainable structural resolution. From this fact, the resolution limit due to the quantum noise attainable by this new method of analysis as well as two important experimental parameters, the number of two-dimensional patterns to be measured (the load for the detector) and the number of pairs of two-dimensional patterns to be analysed (the load for the computer), are derived as a function of the incident X-ray intensity and quantities characterizing the target molecule.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Tokuhisa, A.Taka, J.Kono, H.Go, N.2012-05-01doi:10.1107/S010876731200493XInternational Union of CrystallographyA new algorithm is developed for reconstructing the high-resolution three-dimensional diffraction intensity function of a globular biological macromolecule from many quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The structural resolution is expressed as a function of the incident X-ray intensity and quantities characterizing the target molecule.enBIOLOGICAL MACROMOLECULES; CLASSIFICATION OF TWO-DIMENSIONAL DIFFRACTION PATTERNS; COMMON INTERSECTING CIRCLES; ATTAINABLE STRUCTURAL RESOLUTIONA new two-step algorithm is developed for reconstructing the three-dimensional diffraction intensity of a globular biological macromolecule from many experimentally measured quantum-noise-limited two-dimensional X-ray laser diffraction patterns, each for an unknown orientation. The first step is classification of the two-dimensional patterns into groups according to the similarity of direction of the incident X-rays with respect to the molecule and an averaging within each group to reduce the noise. The second step is detection of common intersecting circles between the signal-enhanced two-dimensional patterns to identify their mutual location in the three-dimensional wavenumber space. The newly developed algorithm enables one to detect a signal for classification in noisy experimental photon-count data with as low as ∼0.1 photons per effective pixel. The wavenumber of such a limiting pixel determines the attainable structural resolution. From this fact, the resolution limit due to the quantum noise attainable by this new method of analysis as well as two important experimental parameters, the number of two-dimensional patterns to be measured (the load for the detector) and the number of pairs of two-dimensional patterns to be analysed (the load for the computer), are derived as a function of the incident X-ray intensity and quantities characterizing the target molecule.text/htmlClassifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function: resolution limit due to the quantum noisetext3682012-05-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papers366med@iucr.org3811600-5724Symétrie et propriétés physiques des cristaux. Par Cécile Malgrange, Christian Ricolleau et Françoise Lefaucheux. Pp. xxii+494. Les Ulis: EDP Sciences et CNRS Éditions, 2011. Prix (broché) EUR 52. ISBN-13: 978-2-7598-0499-3. (In French.)
http://scripts.iucr.org/cgi-bin/paper?pf0092
Copyright (c) 2012 International Union of Crystallographyurn:issn:0108-7673Paufler, P.2012-05-01doi:10.1107/S0108767312007106International Union of CrystallographyenBOOK RECEIVEDtext/htmlSymétrie et propriétés physiques des cristaux. Par Cécile Malgrange, Christian Ricolleau et Françoise Lefaucheux. Pp. xxii+494. Les Ulis: EDP Sciences et CNRS Éditions, 2011. Prix (broché) EUR 52. ISBN-13: 978-2-7598-0499-3. (In French.)text3682012-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2012 International Union of Crystallography0108-7673books receivedmed@iucr.org1600-5724Notes for authors 2012
http://scripts.iucr.org/cgi-bin/paper?me0454
urn:issn:0108-7673IUCr Editorial Office2012-03-01doi:10.1107/S0108767311047209International Union of CrystallographyNotes for authors.enNOTES FOR AUTHORStext/htmlNotes for authors 2012text682Acta Crystallographica Section A: Foundations of Crystallography2012-03-01307international union of crystallography0108-7673med@iucr.org3111600-5724Laue centennial
http://scripts.iucr.org/cgi-bin/paper?wx0004
urn:issn:0108-7673Schmahl, W.W.Steurer, W.2012-01-01doi:10.1107/S0108767311041353International Union of CrystallographyA selection of articles from the Laue symposium to be held during the 20th Annual Meeting of the German Crystallographic Society (DGK) in Munich, 12–15 March 2012, are introduced.enEDITORIAL; LAUE CENTENNIALtext/htmlLaue centennialtext681Acta Crystallographica Section A: Foundations of Crystallography2012-01-011research papers0108-7673med@iucr.org21600-5724Grazing-incidence small-angle X-ray scattering: application to the study of quantum dot lattices
http://scripts.iucr.org/cgi-bin/paper?ib5003
The ordering of quantum dots in three-dimensional quantum dot lattices is investigated by grazing-incidence small-angle X-ray scattering (GISAXS). Theoretical models describing GISAXS intensity distributions for three general classes of lattices of quantum dots are proposed. The classes differ in the type of disorder of the positions of the quantum dots. The models enable full structure determination, including lattice type, lattice parameters, the type and degree of disorder in the quantum dot positions and the distributions of the quantum dot sizes. Applications of the developed models are demonstrated using experimentally measured data from several types of quantum dot lattices formed by a self-assembly process.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Buljan, M.Radić, N.Bernstorff, S.Dražić, G.Bogdanović-Radović, I.Holý, V.2012-01-01doi:10.1107/S0108767311040104International Union of CrystallographyThe modelling of grazing-incidence small-angle X-ray scattering (GISAXS) from three-dimensional quantum dot lattices is described.enGRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING; GISAXS; QUANTUM DOT LATTICES; SELF-ASSEMBLYThe ordering of quantum dots in three-dimensional quantum dot lattices is investigated by grazing-incidence small-angle X-ray scattering (GISAXS). Theoretical models describing GISAXS intensity distributions for three general classes of lattices of quantum dots are proposed. The classes differ in the type of disorder of the positions of the quantum dots. The models enable full structure determination, including lattice type, lattice parameters, the type and degree of disorder in the quantum dot positions and the distributions of the quantum dot sizes. Applications of the developed models are demonstrated using experimentally measured data from several types of quantum dot lattices formed by a self-assembly process.text/htmlGrazing-incidence small-angle X-ray scattering: application to the study of quantum dot latticestext1682012-01-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papersmed@iucr.org1600-5724Optical properties of X-rays – dynamical diffractionThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Authier (2012). Z. Kristallogr. 227, 36–51].
http://scripts.iucr.org/cgi-bin/paper?wx0006
The first attempts at measuring the optical properties of X-rays such as refraction, reflection and diffraction are described. The main ideas forming the basis of Ewald's thesis in 1912 are then summarized. The first extension of Ewald's thesis to the X-ray case is the introduction of the reciprocal lattice. In the next step, the principles of the three versions of the dynamical theory of diffraction, by Darwin, Ewald and Laue, are given. It is shown how the comparison of the dynamical and geometrical theories of diffraction led Darwin to propose his extinction theory. The main optical properties of X-ray wavefields at the Bragg incidence are then reviewed: Pendellösung, shift of the Bragg peak, fine structure of Kossel lines, standing waves, anomalous absorption, paths of wavefields inside the crystal, Borrmann fan and double refraction. Lastly, some of the modern applications of the dynamical theory are briefly outlined: X-ray topography, location of adsorbed atoms at crystal surfaces, optical devices for synchrotron radiation and X-ray interferometry.urn:issn:0108-7673Authier, A.2012-01-01doi:10.1107/S0108767311040219International Union of CrystallographyAttempts to observe refraction or diffraction of X-rays were unsuccessful until the discovery of X-ray diffraction in 1912 by Friedrich, Knipping and Laue. The index of refraction of matter for X-rays and the specific optical properties of X-rays when they are Bragg-diffracted by a perfect crystal, such as total reflection, anomalous absorption, Pendellösung and double refraction, are best understood using the dynamical theory of diffraction.enX-RAY DIFFRACTION; DYNAMICAL THEORY; KOSSEL LINES; REFRACTIVE INDEX; X-RAY INTERFEROMETERSThe first attempts at measuring the optical properties of X-rays such as refraction, reflection and diffraction are described. The main ideas forming the basis of Ewald's thesis in 1912 are then summarized. The first extension of Ewald's thesis to the X-ray case is the introduction of the reciprocal lattice. In the next step, the principles of the three versions of the dynamical theory of diffraction, by Darwin, Ewald and Laue, are given. It is shown how the comparison of the dynamical and geometrical theories of diffraction led Darwin to propose his extinction theory. The main optical properties of X-ray wavefields at the Bragg incidence are then reviewed: Pendellösung, shift of the Bragg peak, fine structure of Kossel lines, standing waves, anomalous absorption, paths of wavefields inside the crystal, Borrmann fan and double refraction. Lastly, some of the modern applications of the dynamical theory are briefly outlined: X-ray topography, location of adsorbed atoms at crystal surfaces, optical devices for synchrotron radiation and X-ray interferometry.text/htmlOptical properties of X-rays – dynamical diffractionThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Authier (2012). Z. Kristallogr. 227, 36–51].text681Acta Crystallographica Section A: Foundations of Crystallography2012-01-0140research papers0108-7673med@iucr.org561600-5724Disputed discovery: the beginnings of X-ray diffraction in crystals in 1912 and its repercussionsThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Eckert (2012). Z. Kristallogr. 227, 27–35].
http://scripts.iucr.org/cgi-bin/paper?wx0005
The discovery of X-ray diffraction is reviewed from the perspective of the contemporary knowledge in 1912 about the nature of X-rays. Laue's inspiration that led to the experiments by Friedrich and Knipping in Sommerfeld's institute was based on erroneous expectations. The ensuing discoveries of the Braggs clarified the phenomenon (although they, too, emerged from dubious assumptions about the nature of X-rays). The early misapprehensions had no impact on the Nobel Prizes to Laue in 1914 and the Braggs in 1915; but when the prizes were finally awarded after the war, the circumstances of `Laue's discovery' gave rise to repercussions. Many years later, they resulted in a dispute about the `myths of origins' of the community of crystallographers.urn:issn:0108-7673Eckert, M.2012-01-01doi:10.1107/S0108767311039985International Union of CrystallographyThe background of `Laue's discovery' and its early repercussions are described. The discovery of X-ray diffraction by crystals was based on misconceptions about the nature of X-rays and the origin of monochromacy observed in the Laue spots.enM. VON LAUE; A. SOMMERFELD; W. H. BRAGG; W. L. BRAGGThe discovery of X-ray diffraction is reviewed from the perspective of the contemporary knowledge in 1912 about the nature of X-rays. Laue's inspiration that led to the experiments by Friedrich and Knipping in Sommerfeld's institute was based on erroneous expectations. The ensuing discoveries of the Braggs clarified the phenomenon (although they, too, emerged from dubious assumptions about the nature of X-rays). The early misapprehensions had no impact on the Nobel Prizes to Laue in 1914 and the Braggs in 1915; but when the prizes were finally awarded after the war, the circumstances of `Laue's discovery' gave rise to repercussions. Many years later, they resulted in a dispute about the `myths of origins' of the community of crystallographers.text/htmlDisputed discovery: the beginnings of X-ray diffraction in crystals in 1912 and its repercussionsThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Eckert (2012). Z. Kristallogr. 227, 27–35].text681Acta Crystallographica Section A: Foundations of Crystallography2012-01-0130research papers0108-7673med@iucr.org391600-5724A multi-dataset data-collection strategy produces better diffraction data
http://scripts.iucr.org/cgi-bin/paper?zm5092
A multi-dataset (MDS) data-collection strategy is proposed and analyzed for macromolecular crystal diffraction data acquisition. The theoretical analysis indicated that the MDS strategy can reduce the standard deviation (background noise) of diffraction data compared with the commonly used single-dataset strategy for a fixed X-ray dose. In order to validate the hypothesis experimentally, a data-quality evaluation process, termed a readiness test of the X-ray data-collection system, was developed. The anomalous signals of sulfur atoms in zinc-free insulin crystals were used as the probe to differentiate the quality of data collected using different data-collection strategies. The data-collection results using home-laboratory-based rotating-anode X-ray and synchrotron X-ray systems indicate that the diffraction data collected with the MDS strategy contain more accurate anomalous signals from sulfur atoms than the data collected with a regular data-collection strategy. In addition, the MDS strategy offered more advantages with respect to radiation-damage-sensitive crystals and better usage of rotating-anode as well as synchrotron X-rays.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Liu, Z.-J.Chen, L.Wu, D.Ding, W.Zhang, H.Zhou, W.Fu, Z.-Q.Wang, B.-C.2011-11-01doi:10.1107/S0108767311037469International Union of CrystallographyTheoretical analysis and experimental validation prove that a multi-dataset data-collection strategy produces better diffraction data. The readiness test is a simple and sensitive method for X-ray data-collection system evaluation and a benchmark.enMULTI-DATASET DATA-COLLECTION STRATEGY; READINESS TESTA multi-dataset (MDS) data-collection strategy is proposed and analyzed for macromolecular crystal diffraction data acquisition. The theoretical analysis indicated that the MDS strategy can reduce the standard deviation (background noise) of diffraction data compared with the commonly used single-dataset strategy for a fixed X-ray dose. In order to validate the hypothesis experimentally, a data-quality evaluation process, termed a readiness test of the X-ray data-collection system, was developed. The anomalous signals of sulfur atoms in zinc-free insulin crystals were used as the probe to differentiate the quality of data collected using different data-collection strategies. The data-collection results using home-laboratory-based rotating-anode X-ray and synchrotron X-ray systems indicate that the diffraction data collected with the MDS strategy contain more accurate anomalous signals from sulfur atoms than the data collected with a regular data-collection strategy. In addition, the MDS strategy offered more advantages with respect to radiation-damage-sensitive crystals and better usage of rotating-anode as well as synchrotron X-rays.text/htmlA multi-dataset data-collection strategy produces better diffraction datatext676http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations of Crystallography2011-11-01544research papers0108-7673med@iucr.org5491600-5724Crystallography from Haüy to Laue: controversies on the molecular and atomistic nature of solidsThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Kubbinga (2012). Z. Kristallogr. 227, 1–26].
http://scripts.iucr.org/cgi-bin/paper?wx0001
The history of crystallography has been assessed in the context of the emergence and spread of the molecular theory. The present paper focuses on the 19th century, which saw the emancipation of crystallography as a science sui generis. Around 1800, Laplace's molecularism called the tune in the various sciences (physics, chemistry, biology, crystallography). In crystallography, two schools opposed each other: that of Weiss, in Berlin, and that of Haüy, in Paris. Symmetry proved essential. It will be shown how the lattice theory arose in an essentially molecular framework and how group theory imposed itself. The salt hydrates suggested the idea of (two or more) superimposed molecular lattices. Gradually it became clear that an ultimate lattice theory ought to be atomic. The experiments of Laue, Friedrich and Knipping confirmed that atomic basis.urn:issn:0108-7673Kubbinga, H.2012-01-01doi:10.1107/S0108767311030315International Union of CrystallographyThe history of crystallography circa 1784–1912 is described.enMOLECULARISM; LATTICE THEORY; ISOMORPHISM; POLYMORPHISM; SYMMETRY; PROJECTION TECHNIQUES; GROUP THEORY; CRYSTAL SYSTEMS; CRYSTAL CLASSES; SPACE LATTICES; DISCOVERY OF X-RAYSThe history of crystallography has been assessed in the context of the emergence and spread of the molecular theory. The present paper focuses on the 19th century, which saw the emancipation of crystallography as a science sui generis. Around 1800, Laplace's molecularism called the tune in the various sciences (physics, chemistry, biology, crystallography). In crystallography, two schools opposed each other: that of Weiss, in Berlin, and that of Haüy, in Paris. Symmetry proved essential. It will be shown how the lattice theory arose in an essentially molecular framework and how group theory imposed itself. The salt hydrates suggested the idea of (two or more) superimposed molecular lattices. Gradually it became clear that an ultimate lattice theory ought to be atomic. The experiments of Laue, Friedrich and Knipping confirmed that atomic basis.text/htmlCrystallography from Haüy to Laue: controversies on the molecular and atomistic nature of solidsThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Kubbinga (2012). Z. Kristallogr. 227, 1–26].text681Acta Crystallographica Section A: Foundations of Crystallography2012-01-013research papers0108-7673med@iucr.org291600-5724The success story of crystallographyThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Schwarzenbach (2012). Z. Kristallogr. 227, 52–62].
http://scripts.iucr.org/cgi-bin/paper?wx0002
Diffractionists usually place the birth of crystallography in 1912 with the first X-ray diffraction experiment of Friedrich, Knipping and Laue. This discovery propelled the mathematical branch of mineralogy to global importance and enabled crystal structure determination. Knowledge of the geometrical structure of matter at atomic resolution had revolutionary consequences for all branches of the natural sciences: physics, chemistry, biology, earth sciences and material science. It is scarcely possible for a single person in a single article to trace and appropriately value all of these developments. This article presents the limited, subjective view of its author and a limited selection of references. The bulk of the article covers the history of X-ray structure determination from the NaCl structure to aperiodic structures and macromolecular structures. The theoretical foundations were available by 1920. The subsequent success of crystallography was then due to the development of diffraction equipment, the theory of the solution of the phase problem, symmetry theory and computers. The many structures becoming known called for the development of crystal chemistry and of data banks. Diffuse scattering from disordered structures without and with partial long-range order allows determination of short-range order. Neutron and electron scattering and diffraction are also mentioned.urn:issn:0108-7673Schwarzenbach, D.2012-01-01doi:10.1107/S0108767311030303International Union of CrystallographyThe development of crystallography starting with Laue's discovery is sketched.enHISTORY; DIFFRACTION; STRUCTURE DETERMINATION; ATOMIC RESOLUTIONDiffractionists usually place the birth of crystallography in 1912 with the first X-ray diffraction experiment of Friedrich, Knipping and Laue. This discovery propelled the mathematical branch of mineralogy to global importance and enabled crystal structure determination. Knowledge of the geometrical structure of matter at atomic resolution had revolutionary consequences for all branches of the natural sciences: physics, chemistry, biology, earth sciences and material science. It is scarcely possible for a single person in a single article to trace and appropriately value all of these developments. This article presents the limited, subjective view of its author and a limited selection of references. The bulk of the article covers the history of X-ray structure determination from the NaCl structure to aperiodic structures and macromolecular structures. The theoretical foundations were available by 1920. The subsequent success of crystallography was then due to the development of diffraction equipment, the theory of the solution of the phase problem, symmetry theory and computers. The many structures becoming known called for the development of crystal chemistry and of data banks. Diffuse scattering from disordered structures without and with partial long-range order allows determination of short-range order. Neutron and electron scattering and diffraction are also mentioned.text/htmlThe success story of crystallographyThis Laue centennial article has also been published in Zeitschrift für Kristallographie [Schwarzenbach (2012). Z. Kristallogr. 227, 52–62].text681Acta Crystallographica Section A: Foundations of Crystallography2012-01-0157research papers0108-7673med@iucr.org671600-5724Fundamentals of Crystallography, 3rd edition. By C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Edited by C. Giacovazzo. IUCr Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011. Pp. xxi + 842. Price (hardback) GBP 90.00. ISBN 978-0-19-957365-3.
http://scripts.iucr.org/cgi-bin/paper?pf0085
Copyright (c) 2011 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2011-11-01doi:10.1107/S0108767311039523International Union of CrystallographyenBOOK REVIEWtext/htmlFundamentals of Crystallography, 3rd edition. By C. Giacovazzo, H. L. Monaco, G. Artioli, D. Viterbo, M. Milaneso, G. Ferraris, G. Gilli, P. Gilli, G. Zanotti and M. Catti. Edited by C. Giacovazzo. IUCr Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011. Pp. xxi + 842. Price (hardback) GBP 90.00. ISBN 978-0-19-957365-3.text676Copyright (c) 2011 International Union of CrystallographyActa Crystallographica Section A: Foundations of Crystallography2011-11-01561book reviews0108-7673med@iucr.org5631600-5724Bayesian algorithms for recovering structure from single-particle diffraction snapshots of unknown orientation: a comparison
http://scripts.iucr.org/cgi-bin/paper?mk5026
The advent of X-ray free-electron lasers promises the possibility to determine the structure of individual particles such as microcrystallites, viruses and biomolecules from single-shot diffraction snapshots obtained before the particle is destroyed by the intense femtosecond pulse. This program requires the ability to determine the orientation of the particle giving rise to each snapshot at signal levels as low as ~10−2 photons per pixel. Two apparently different approaches have recently demonstrated this capability. Here we show they represent different implementations of the same fundamental approach, and identify the primary factors limiting their performance.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Moths, B.Ourmazd, A.2011-09-01doi:10.1107/S0108767311019611International Union of CrystallographyX-ray free-electron lasers are being used to determine the three-dimensional structure of objects from random snapshots. The two apparently very different Bayesian algorithms capable of performing this at ultra-low signal are fundamentally the same.enX-RAY SCATTERING; SINGLE-PARTICLE STRUCTURE DETERMINATIONThe advent of X-ray free-electron lasers promises the possibility to determine the structure of individual particles such as microcrystallites, viruses and biomolecules from single-shot diffraction snapshots obtained before the particle is destroyed by the intense femtosecond pulse. This program requires the ability to determine the orientation of the particle giving rise to each snapshot at signal levels as low as ~10−2 photons per pixel. Two apparently different approaches have recently demonstrated this capability. Here we show they represent different implementations of the same fundamental approach, and identify the primary factors limiting their performance.text/htmlBayesian algorithms for recovering structure from single-particle diffraction snapshots of unknown orientation: a comparisontext5672011-09-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papersmed@iucr.org1600-5724Ninth Ewald Prize
http://scripts.iucr.org/cgi-bin/paper?es0385
The ninth Ewald Prize has been awarded to Professor E. Dodson, Professor C. Giacovazzo and Professor G. M. Sheldrick for the enormous impact they have made on structural crystallography.urn:issn:0108-7673Dacombe, M.2011-07-01doi:10.1107/S0108767311018526International Union of CrystallographyThe winners of the ninth Ewald Prize are announced.enEWALD PRIZEThe ninth Ewald Prize has been awarded to Professor E. Dodson, Professor C. Giacovazzo and Professor G. M. Sheldrick for the enormous impact they have made on structural crystallography.text/htmlNinth Ewald Prizetext674Acta Crystallographica Section A: Foundations of Crystallography2011-07-01419international union of crystallography0108-7673med@iucr.org4191600-5724Response to Olczak's comment on Probability density functions of the average and difference intensities of Friedel opposites
http://scripts.iucr.org/cgi-bin/paper?sh0191
A response is given to to Olczak's comment about the discussion of probability density functions (p.d.f.s) and simulations of Friedel intensity differences in Shmueli & Flack [Acta Cryst. (2010), A66, 669–675].Copyright (c) 2011 International Union of Crystallographyurn:issn:0108-7673Shmueli, U.Flack, H.2011-05-01doi:10.1107/S0108767311007951International Union of CrystallographyResponse to Olczak's comment on Shmueli & Flack [Acta Cryst. (2010), A66, 669–675].enPROBABILITY DENSITY FUNCTIONS; FRIEDEL OPPOSITESA response is given to to Olczak's comment about the discussion of probability density functions (p.d.f.s) and simulations of Friedel intensity differences in Shmueli & Flack [Acta Cryst. (2010), A66, 669–675].text/htmlResponse to Olczak's comment on Probability density functions of the average and difference intensities of Friedel oppositestext3672011-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2011 International Union of Crystallography0108-7673letters to the editor318med@iucr.org3181600-5724Comment on Probability density functions of the average and difference intensities of Friedel opposites by Shmueli & Flack (2010)
http://scripts.iucr.org/cgi-bin/paper?sh5123
A comment is made on the discussion of probability density functions (p.d.f.s) and simulations of Friedel intensity differences in Shmueli & Flack [Acta Cryst. (2010), A66, 669–675].Copyright (c) 2011 International Union of Crystallographyurn:issn:0108-7673Olczak, A.2011-05-01doi:10.1107/S0108767311007896International Union of CrystallographyComment on Shmueli & Flack [Acta Cryst. (2010), A66, 669–675].enPROBABILITY DENSITY FUNCTIONS; FRIEDEL OPPOSITESA comment is made on the discussion of probability density functions (p.d.f.s) and simulations of Friedel intensity differences in Shmueli & Flack [Acta Cryst. (2010), A66, 669–675].text/htmlComment on Probability density functions of the average and difference intensities of Friedel opposites by Shmueli & Flack (2010)text3672011-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2011 International Union of Crystallography0108-7673letters to the editor315med@iucr.org3171600-5724Exact direct-space asymmetric units for the 230 crystallographic space groups
http://scripts.iucr.org/cgi-bin/paper?pz5088
It is well known that the direct-space asymmetric unit definitions found in the International Tables for Crystallography, Volume A, are inexact at the borders. Face- and edge-specific sub-conditions have to be added to remove parts redundant under symmetry. This paper introduces a concise geometric notation for asymmetric unit conditions. The notation is the foundation for a reference table of exact direct-space asymmetric unit definitions for the 230 crystallographic space-group types. The change-of-basis transformation law for the conditions is derived, which allows the information from the reference table to be used for any space-group setting. We also show how the vertices of an asymmetric unit can easily be computed from the information in the reference table.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Grosse-Kunstleve, R.W.Wong, B.Mustyakimov, M.Adams, P.D.2011-05-01doi:10.1107/S0108767311007008International Union of CrystallographyA reference table of exact direct-space asymmetric units for the 230 crystallographic space groups is presented, based on a new geometric notation for asymmetric unit conditions.enASYMMETRIC UNIT; DIRECT SPACE; SPACE GROUPSIt is well known that the direct-space asymmetric unit definitions found in the International Tables for Crystallography, Volume A, are inexact at the borders. Face- and edge-specific sub-conditions have to be added to remove parts redundant under symmetry. This paper introduces a concise geometric notation for asymmetric unit conditions. The notation is the foundation for a reference table of exact direct-space asymmetric unit definitions for the 230 crystallographic space-group types. The change-of-basis transformation law for the conditions is derived, which allows the information from the reference table to be used for any space-group setting. We also show how the vertices of an asymmetric unit can easily be computed from the information in the reference table.text/htmlExact direct-space asymmetric units for the 230 crystallographic space groupstext3672011-05-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papers269med@iucr.org2751600-5724Translation calibration of inverse-kappa goniometers in macromolecular crystallography
http://scripts.iucr.org/cgi-bin/paper?zm5081
Precise and convenient crystal reorientation is of experimental importance in macromolecular crystallography (MX). The development of multi-axis goniometers, such as the ESRF/EMBL mini-κ, necessitates the corresponding development of calibration procedures that can be used for the setup, maintenance and troubleshooting of such devices. While traditional multi-axis goniometers require all rotation axes to intersect the unique point of the sample position, recently developed miniaturized instruments for sample reorientation in MX are not as restricted. However, the samples must always be re-centred following a change in orientation. To overcome this inconvenience and allow the use of multi-axis goniometers without the fundamental restriction of having all axes intersecting in the same point, an automatic translation correction protocol has been developed for such instruments. It requires precise information about the direction and location of the rotation axes. To measure and supply this information, a general, easy-to-perform translation calibration (TC) procedure has also been developed. The TC procedure is routinely performed on most MX beamlines at the ESRF and some results are presented for reference.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Brockhauser, S.White, K.I.McCarthy, A.A.Ravelli, R.B.G.2011-05-01doi:10.1107/S0108767311004831International Union of CrystallographyA rapid, easy-to-perform translation calibration procedure has been developed for use with the EMBL/ESRF mini-κ goniometer head and for other inverse-kappa goniometers designed for macromolecular crystallography. Regular calibration ensures the precision of experiments that rely on many degrees of freedom in crystal reorientation.enKAPPA GONIOMETER; MACROMOLECULAR CRYSTALLOGRAPHY; REORIENTATION; CALIBRATIONPrecise and convenient crystal reorientation is of experimental importance in macromolecular crystallography (MX). The development of multi-axis goniometers, such as the ESRF/EMBL mini-κ, necessitates the corresponding development of calibration procedures that can be used for the setup, maintenance and troubleshooting of such devices. While traditional multi-axis goniometers require all rotation axes to intersect the unique point of the sample position, recently developed miniaturized instruments for sample reorientation in MX are not as restricted. However, the samples must always be re-centred following a change in orientation. To overcome this inconvenience and allow the use of multi-axis goniometers without the fundamental restriction of having all axes intersecting in the same point, an automatic translation correction protocol has been developed for such instruments. It requires precise information about the direction and location of the rotation axes. To measure and supply this information, a general, easy-to-perform translation calibration (TC) procedure has also been developed. The TC procedure is routinely performed on most MX beamlines at the ESRF and some results are presented for reference.text/htmlTranslation calibration of inverse-kappa goniometers in macromolecular crystallographytext3672011-05-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papers219med@iucr.org2281600-5724On the allowed values for the triclinic unit-cell angles
http://scripts.iucr.org/cgi-bin/paper?au5114
This short article questions and investigates the possible range of values for the three angles of a unit cell in the triclinic system. Although no constraints are reported in manuals and tables for crystallography, the three angles are not really independent; the range of allowed values is calculated and presented in this paper.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Foadi, J.Evans, G.2011-01-01doi:10.1107/S0108767310044296International Union of CrystallographyThe possible range of angles for a triclinic unit cell are explored in detail.enTRICLINIC UNIT CELLS; UNIT-CELL ANGLES; TRIHEDRAL ANGLES; GENERALIZED SINEThis short article questions and investigates the possible range of values for the three angles of a unit cell in the triclinic system. Although no constraints are reported in manuals and tables for crystallography, the three angles are not really independent; the range of allowed values is calculated and presented in this paper.text/htmlOn the allowed values for the triclinic unit-cell anglestext1672011-01-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673short communications93med@iucr.org951600-5724Geometric properties of nucleic acids with potential for autobuilding
http://scripts.iucr.org/cgi-bin/paper?sc5036
Medium- to high-resolution X-ray structures of DNA and RNA molecules were investigated to find geometric properties useful for automated model building in crystallographic electron-density maps. We describe a simple method, starting from a list of electron-density `blobs', for identifying backbone phosphates and nucleic acid bases based on properties of the local electron-density distribution. This knowledge should be useful for the automated building of nucleic acid models into electron-density maps. We show that the distances and angles involving C1′ and the P atoms, using the pseudo-torsion angles \eta' and \theta\,' that describe the …P—C1′—P—C1′… chain, provide a promising basis for building the nucleic acid polymer. These quantities show reasonably narrow distributions with asymmetry that should allow the direction of the phosphate backbone to be established.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Gruene, T.Sheldrick, G.M.2011-01-01doi:10.1107/S0108767310039140International Union of CrystallographyAlgorithms and geometrical properties are described for the automated building of nucleic acids in experimental electron density.enNUCLEIC ACIDS; AUTOBUILDING; GEOMETRIC PROPERTIES; ELECTRON-DENSITY DISTRIBUTIONMedium- to high-resolution X-ray structures of DNA and RNA molecules were investigated to find geometric properties useful for automated model building in crystallographic electron-density maps. We describe a simple method, starting from a list of electron-density `blobs', for identifying backbone phosphates and nucleic acid bases based on properties of the local electron-density distribution. This knowledge should be useful for the automated building of nucleic acid models into electron-density maps. We show that the distances and angles involving C1′ and the P atoms, using the pseudo-torsion angles \eta' and \theta\,' that describe the …P—C1′—P—C1′… chain, provide a promising basis for building the nucleic acid polymer. These quantities show reasonably narrow distributions with asymmetry that should allow the direction of the phosphate backbone to be established.text/htmlGeometric properties of nucleic acids with potential for autobuildingtext671http://creativecommons.org/licenses/by/2.0/ukActa Crystallographica Section A: Foundations of Crystallography2011-01-011research papers0108-7673med@iucr.org81600-5724Crystallography of Quasicrystals. By Walter Steurer and Sofia Deloudi. Springer Series in Materials Sciences No. 126. Springer, 2009. Pp. xiv + 384. Price (hardback) EUR 128.35. ISBN 978-3-642-01898-5, e-ISBN 978-3-642-01899-2, doi 10.1007/978-3-642-01899-2.
http://scripts.iucr.org/cgi-bin/paper?pf0078
Copyright (c) 2010 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2010-09-01doi:10.1107/S0108767310021239International Union of CrystallographyenBOOK REVIEWtext/htmlCrystallography of Quasicrystals. By Walter Steurer and Sofia Deloudi. Springer Series in Materials Sciences No. 126. Springer, 2009. Pp. xiv + 384. Price (hardback) EUR 128.35. ISBN 978-3-642-01898-5, e-ISBN 978-3-642-01899-2, doi 10.1007/978-3-642-01899-2.text5662010-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2010 International Union of Crystallography0108-7673book reviews629med@iucr.org6301600-5724Mode crystallography of distorted structures
http://scripts.iucr.org/cgi-bin/paper?sh5107
The description of displacive distorted structures in terms of symmetry-adapted modes is reviewed. A specific parameterization of the symmetry-mode decomposition of these pseudosymmetric structures defined on the setting of the experimental space group is proposed. This approach closely follows crystallographic conventions and permits a straightforward transformation between symmetry-mode and conventional descriptions of the structures. Multiple examples are presented showing the insight provided by the symmetry-mode approach. The methodology is shown at work, illustrating its various possibilities for improving the characterization of distorted structures, for example: detection of hidden structural correlations, identification of fundamental and marginal degrees of freedom, reduction of the effective number of atomic positional parameters, quantitative comparison of structures with the same or different space group, detection of false refinement minima, systematic characterization of thermal behavior, rationalization of phase diagrams and various symmetries in families of compounds etc. The close relation of the symmetry-mode description with the superspace formalism applied to commensurate superstructures is also discussed. Finally, the application of this methodology in the field of ab initio or first-principles calculations is outlined. At present, there are several freely available user-friendly computer tools for performing automatic symmetry-mode analyses. The use of these programs does not require a deep knowledge of group theory and can be applied either a posteriori to analyze a given distorted structure or a priori to parameterize the structure to be determined. It is hoped that this article will encourage the use of these tools. All the examples presented here have been worked out using the program AMPLIMODES [Orobengoa et al. (2009). J. Appl. Cryst. 42, 820–833].Copyright (c) 2010 International Union of Crystallographyurn:issn:0108-7673Perez-Mato, J.M.Orobengoa, D.Aroyo, M.I.2010-09-01doi:10.1107/S0108767310016247International Union of CrystallographySymmetry-mode decomposition of displacive distorted structures and its applications are reviewed in the light of new freely available software. The advantages of a parameterization in terms of symmetry-adapted collective coordinates are illustrated with multiple examples.enDISTORTED STRUCTURES; SYMMETRY-ADAPTED MODES; SYMMETRY-MODE DECOMPOSITION; AMPLIMODESThe description of displacive distorted structures in terms of symmetry-adapted modes is reviewed. A specific parameterization of the symmetry-mode decomposition of these pseudosymmetric structures defined on the setting of the experimental space group is proposed. This approach closely follows crystallographic conventions and permits a straightforward transformation between symmetry-mode and conventional descriptions of the structures. Multiple examples are presented showing the insight provided by the symmetry-mode approach. The methodology is shown at work, illustrating its various possibilities for improving the characterization of distorted structures, for example: detection of hidden structural correlations, identification of fundamental and marginal degrees of freedom, reduction of the effective number of atomic positional parameters, quantitative comparison of structures with the same or different space group, detection of false refinement minima, systematic characterization of thermal behavior, rationalization of phase diagrams and various symmetries in families of compounds etc. The close relation of the symmetry-mode description with the superspace formalism applied to commensurate superstructures is also discussed. Finally, the application of this methodology in the field of ab initio or first-principles calculations is outlined. At present, there are several freely available user-friendly computer tools for performing automatic symmetry-mode analyses. The use of these programs does not require a deep knowledge of group theory and can be applied either a posteriori to analyze a given distorted structure or a priori to parameterize the structure to be determined. It is hoped that this article will encourage the use of these tools. All the examples presented here have been worked out using the program AMPLIMODES [Orobengoa et al. (2009). J. Appl. Cryst. 42, 820–833].text/htmlMode crystallography of distorted structurestext5662010-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2010 International Union of Crystallography0108-7673lead articles558med@iucr.org5901600-5724Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches
http://scripts.iucr.org/cgi-bin/paper?xd5026
Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein's resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein's conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein's reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Westenhoff, S.Nazarenko, E.Malmerberg, E.Davidsson, J.Katona, G.Neutze, R.2010-03-01doi:10.1107/S0108767309054361International Union of CrystallographyTime-resolved structural studies of proteins have undergone several significant developments during the last decade. Recent developments using time-resolved X-ray methods, such as time-resolved Laue diffraction, low-temperature intermediate trapping, time-resolved wide-angle X-ray scattering and time-resolved X-ray absorption spectroscopy, are reviewed.enTIME-RESOLVED DIFFRACTION; STRUCTURAL BIOLOGY; PROTEIN STRUCTURAL DYNAMICS; LAUE DIFFRACTION; KINETIC CRYSTALLOGRAPHY; WAXS; XASProteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein's resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein's conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein's reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.text/htmlTime-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approachestext2662010-03-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papers207med@iucr.org2191600-5724Five-dimensional crystallography
http://scripts.iucr.org/cgi-bin/paper?xd5019
A method for determining a comprehensive chemical kinetic mechanism in macromolecular reactions is presented. The method is based on five-dimensional crystallography, where, in addition to space and time, temperature is also taken into consideration and an analysis based on singular value decomposition is applied. First results of such a time-resolved crystallographic study are presented. Temperature-dependent time-resolved X-ray diffraction measurements were conducted on the newly upgraded BioCARS 14-ID-B beamline at the Advanced Photon Source and aimed at elucidating a comprehensive kinetic mechanism of the photoactive yellow protein photocycle. Extensive time series of crystallographic data were collected at two temperatures, 293 K and 303 K. Relaxation times of the reaction extracted from these time series exhibit measurable differences for the two temperatures, hence demonstrating that five-dimensional crystallography is feasible.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0108-7673Schmidt, M.Graber, T.Henning, R.Srajer, V.2010-03-01doi:10.1107/S0108767309054166International Union of CrystallographyHere it is demonstrated how five-dimensional crystallography can be used to determine a comprehensive chemical kinetic mechanism in concert with the atomic structures of transient intermediates that form and decay during the course of the reaction.enTIME-RESOLVED CRYSTALLOGRAPHY; CHEMICAL KINETICS; PROTEIN STRUCTURE; TEMPERATURE DEPENDENCEA method for determining a comprehensive chemical kinetic mechanism in macromolecular reactions is presented. The method is based on five-dimensional crystallography, where, in addition to space and time, temperature is also taken into consideration and an analysis based on singular value decomposition is applied. First results of such a time-resolved crystallographic study are presented. Temperature-dependent time-resolved X-ray diffraction measurements were conducted on the newly upgraded BioCARS 14-ID-B beamline at the Advanced Photon Source and aimed at elucidating a comprehensive kinetic mechanism of the photoactive yellow protein photocycle. Extensive time series of crystallographic data were collected at two temperatures, 293 K and 303 K. Relaxation times of the reaction extracted from these time series exhibit measurable differences for the two temperatures, hence demonstrating that five-dimensional crystallography is feasible.text/htmlFive-dimensional crystallographytext2662010-03-01Acta Crystallographica Section A: Foundations of Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0108-7673research papers198med@iucr.org2061600-5724The birth of the European Crystallographic Committee (ECC) and of the European Crystallographic Meetings (ECMs)
http://scripts.iucr.org/cgi-bin/paper?sh5098
At ECM25, held in Istanbul, Turkey, on 16–21 August 2009, the 25th anniversary of the European Crystallographic Meetings was celebrated. In this article, it is recalled how the idea of coordinating international meetings on crystallography in Europe was put forward at a meeting held in Manchester, UK, in April 1971, and it is explained how the European Crystallographic Committee was established for that purpose during the Ninth IUCr Congress in Kyoto, in 1972. The organization of the first European Crystallographic Meeting, ECM1, held in Bordeaux, France, in 1973, is briefly described and the evolution of the main topics of the scientific programme from that time to ECM25 is commented upon.Copyright (c) 2010 International Union of Crystallographyurn:issn:0108-7673Authier, A.2010-01-01doi:10.1107/S0108767309041853International Union of CrystallographyThis article describes the circumstances of the establishment of the European Crystallographic Committee, now the European Crystallographic Association, a regional associate of the IUCr, and of the European Crystallographic Meetings.enEUROPEAN CRYSTALLOGRAPHIC COMMITTEE; EUROPEAN CRYSTALLOGRAPHIC MEETINGS; EUROPEAN CRYSTALLOGRAPHIC ASSOCIATIONAt ECM25, held in Istanbul, Turkey, on 16–21 August 2009, the 25th anniversary of the European Crystallographic Meetings was celebrated. In this article, it is recalled how the idea of coordinating international meetings on crystallography in Europe was put forward at a meeting held in Manchester, UK, in April 1971, and it is explained how the European Crystallographic Committee was established for that purpose during the Ninth IUCr Congress in Kyoto, in 1972. The organization of the first European Crystallographic Meeting, ECM1, held in Bordeaux, France, in 1973, is briefly described and the evolution of the main topics of the scientific programme from that time to ECM25 is commented upon.text/htmlThe birth of the European Crystallographic Committee (ECC) and of the European Crystallographic Meetings (ECMs)text1662010-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2010 International Union of Crystallography0108-7673feature articles1med@iucr.org41600-5724Foundations of Crystallography with Computer Applications. By Maureen M. Julian. Boca Raton: CRC Press, 2008. Pp. xxvi + 340. Price (hardback) GBP 55.00. ISBN 978-1-4200-6075-1.
http://scripts.iucr.org/cgi-bin/paper?pf0074
Copyright (c) 2009 International Union of Crystallographyurn:issn:0108-7673Aroyo, M.I.2009-11-01doi:10.1107/S0108767309036125International Union of CrystallographyenBOOK REVIEWtext/htmlFoundations of Crystallography with Computer Applications. By Maureen M. Julian. Boca Raton: CRC Press, 2008. Pp. xxvi + 340. Price (hardback) GBP 55.00. ISBN 978-1-4200-6075-1.text6652009-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2009 International Union of Crystallography0108-7673book reviews543med@iucr.org5451600-572460 years of IUCr journals
http://scripts.iucr.org/cgi-bin/paper?sh5087
In the 60 years since its birth in 1948, the number of journals published by the International Union of Crystallography has risen from one to eight. A brief account of the history of the forerunner of the IUCr journals, Zeitschrift für Kristallographie, is given. The context of the birth of the IUCr and the first of its journals, Acta Crystallographica, is recalled. The circumstances which led to the growth of Acta into several sections, at first A and B then, successively, C, D, E and F, and the launch of two new journals, the Journal of Applied Crystallography and the Journal of Synchrotron Radiation, are described. The transition from print-on-paper to electronic journals is also remembered.Copyright (c) 2009 International Union of Crystallographyurn:issn:0108-7673Authier, A.2009-05-01doi:10.1107/S0108767309007235International Union of CrystallographyThe birth and growth of the publications and journals of the International Union of Crystallography from 1948 to 2008 are described. Details are given of the pre-war history that led up to their creation and development.enPUBLISHING; ACTA CRYSTALLOGRAPHICA; JOURNAL OF APPLIED CRYSTALLOGRAPHY; JOURNAL OF SYNCHROTRON RADIATION; INTERNATIONAL TABLES FOR CRYSTALLOGRAPHY; INTERNATIONAL UNION OF CRYSTALLOGRAPHYIn the 60 years since its birth in 1948, the number of journals published by the International Union of Crystallography has risen from one to eight. A brief account of the history of the forerunner of the IUCr journals, Zeitschrift für Kristallographie, is given. The context of the birth of the IUCr and the first of its journals, Acta Crystallographica, is recalled. The circumstances which led to the growth of Acta into several sections, at first A and B then, successively, C, D, E and F, and the launch of two new journals, the Journal of Applied Crystallography and the Journal of Synchrotron Radiation, are described. The transition from print-on-paper to electronic journals is also remembered.text/html60 years of IUCr journalstext3652009-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2009 International Union of Crystallography0108-7673feature articles167med@iucr.org1821600-5724Crystallography and the World of Symmetry. By Sanat K. Chatterjee. Springer Series in Materials Sciences, No. 113. Springer, 2008. Pp. xi + 150. Price (hardback) GBP 87.00. ISBN 978-3-540-69898-2.
http://scripts.iucr.org/cgi-bin/paper?pf0070
Copyright (c) 2009 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2009-03-01doi:10.1107/S0108767309002013International Union of CrystallographyenBOOK REVIEWtext/htmlCrystallography and the World of Symmetry. By Sanat K. Chatterjee. Springer Series in Materials Sciences, No. 113. Springer, 2008. Pp. xi + 150. Price (hardback) GBP 87.00. ISBN 978-3-540-69898-2.text2652009-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2009 International Union of Crystallography0108-7673book reviews164med@iucr.org1661600-5724Three-dimensional Euclidean nets from two-dimensional hyperbolic tilings: kaleidoscopic examples
http://scripts.iucr.org/cgi-bin/paper?sh5079
We present a method for geometric construction of periodic three-dimensional Euclidean nets by projecting two-dimensional hyperbolic tilings onto a family of triply periodic minimal surfaces (TPMSs). Our techniques extend the combinatorial tiling theory of Dress, Huson & Delgado-Friedrichs to enumerate simple reticulations of these TPMSs. We include a taxonomy of all networks arising from kaleidoscopic hyperbolic tilings with up to two distinct tile types (and their duals, with two distinct vertices), mapped to three related TPMSs, namely Schwarz's primitive (P) and diamond (D) surfaces, and Schoen's gyroid (G).Copyright (c) 2009 International Union of Crystallographyurn:issn:0108-7673Ramsden, S.J.Robins, V.Hyde, S.T.2009-03-01doi:10.1107/S0108767308040592International Union of CrystallographySystematic enumeration of tilings of the two-dimensional hyperbolic plane leads to ab initio construction of triply periodic nets via projection of the tilings onto triply periodic minimal surfaces. The technique is described in detail for kaleidoscopic tilings, projected onto the P, D and G (gyroid) minimal surfaces.enTHREE-DIMENSIONAL EUCLIDEAN NETS; TWO-DIMENSIONAL HYPERBOLIC TILINGS; TRIPLY PERIODIC MINIMAL SURFACES; KALEIDOSCOPIC HYPERBOLIC TILINGSWe present a method for geometric construction of periodic three-dimensional Euclidean nets by projecting two-dimensional hyperbolic tilings onto a family of triply periodic minimal surfaces (TPMSs). Our techniques extend the combinatorial tiling theory of Dress, Huson & Delgado-Friedrichs to enumerate simple reticulations of these TPMSs. We include a taxonomy of all networks arising from kaleidoscopic hyperbolic tilings with up to two distinct tile types (and their duals, with two distinct vertices), mapped to three related TPMSs, namely Schwarz's primitive (P) and diamond (D) surfaces, and Schoen's gyroid (G).text/htmlThree-dimensional Euclidean nets from two-dimensional hyperbolic tilings: kaleidoscopic examplestext2652009-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2009 International Union of Crystallography0108-7673lead articles81med@iucr.org1081600-5724Powder Diffraction. Theory and Practice. Edited by R. E. Dinnebier and S. J. L. Billinge. Cambridge: RSC Publishing, 2008. Pp. xxi + 582. Price (hardcover): GBP 59.00. ISBN (online): 978-1-84755-823-7; ISBN (print): 978-0-85404-231-9.
http://scripts.iucr.org/cgi-bin/paper?pf0068
Copyright (c) 2009 International Union of Crystallographyurn:issn:0108-7673Garnier, E.2009-01-01doi:10.1107/S010876730802850XInternational Union of CrystallographyenBOOK REVIEWtext/htmlPowder Diffraction. Theory and Practice. Edited by R. E. Dinnebier and S. J. L. Billinge. Cambridge: RSC Publishing, 2008. Pp. xxi + 582. Price (hardcover): GBP 59.00. ISBN (online): 978-1-84755-823-7; ISBN (print): 978-0-85404-231-9.text1652009-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2009 International Union of Crystallography0108-7673book reviews51med@iucr.org511600-5724Advanced structural inorganic chemistry. IUCr Texts on Crystallography No. 10. By Wai-Kee Li, Gong-Du Zhou and Thomas Chung Wai Mak. Oxford: Oxford University Press, 2008. Pp. xx + 819. Price (paperback) GBP 37.50. ISBN 978-0-19-921695-6.
http://scripts.iucr.org/cgi-bin/paper?pf0065
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Müller, U.2008-07-01doi:10.1107/S0108767308017042International Union of CrystallographyenBOOK REVIEWtext/htmlAdvanced structural inorganic chemistry. IUCr Texts on Crystallography No. 10. By Wai-Kee Li, Gong-Du Zhou and Thomas Chung Wai Mak. Oxford: Oxford University Press, 2008. Pp. xx + 819. Price (paperback) GBP 37.50. ISBN 978-0-19-921695-6.text4642008-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673book reviews513med@iucr.org5141600-5724Aperiodic crystals: from modulated phases to quasicrystals. By T. Janssen, G. Chapuis, and M. de Boissieu. IUCr Monographs on Crystallography, No. 20. Oxford: IUCr/Oxford University Press, 2007. Pp. 466. Price GBP 75.00. ISBN 978-0-19-856777-6.
http://scripts.iucr.org/cgi-bin/paper?pf0060
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Schreiber, M.2008-05-01doi:10.1107/S0108767308009343International Union of CrystallographyenBOOK REVIEWtext/htmlAperiodic crystals: from modulated phases to quasicrystals. By T. Janssen, G. Chapuis, and M. de Boissieu. IUCr Monographs on Crystallography, No. 20. Oxford: IUCr/Oxford University Press, 2007. Pp. 466. Price GBP 75.00. ISBN 978-0-19-856777-6.text3642008-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673book reviews433med@iucr.org4341600-5724Out of the shadows. Contributions of twentieth-century women to physics. Edited by Nina Byers and Gary Williams. Cambridge: Cambridge University Press, 2006. Pp. xxv + 471. Price (hardback) GBP 30.00. ISBN-13 978-0-521-82197-1.
http://scripts.iucr.org/cgi-bin/paper?pf0054
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Reich, K.2008-05-01doi:10.1107/S0108767308006880International Union of CrystallographyenBOOK REVIEWtext/htmlOut of the shadows. Contributions of twentieth-century women to physics. Edited by Nina Byers and Gary Williams. Cambridge: Cambridge University Press, 2006. Pp. xxv + 471. Price (hardback) GBP 30.00. ISBN-13 978-0-521-82197-1.text3642008-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673book reviews432med@iucr.org4321600-5724J. D. Bernal. The sage of science. By Andrew Brown. Pp. 576. Oxford: Oxford University Press, 2007. Price (paperback) GBP 12.99. ISBN 978-0-19-920565-3
http://scripts.iucr.org/cgi-bin/paper?pf0058
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Dodson, G.2008-03-01doi:10.1107/S0108767308002407International Union of CrystallographyenBOOK REVIEWtext/htmlJ. D. Bernal. The sage of science. By Andrew Brown. Pp. 576. Oxford: Oxford University Press, 2007. Price (paperback) GBP 12.99. ISBN 978-0-19-920565-3text2642008-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673book reviews349med@iucr.org3511600-5724Ewald Prize Award
http://scripts.iucr.org/cgi-bin/paper?es0363
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-76732008-03-01doi:10.1107/S0108767308002572International Union of CrystallographyenEWALD PRIZEtext/htmlEwald Prize Awardtext2642008-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673international union of crystallography352med@iucr.org3521600-5724Inorganic structural chemistry. By Ulrich Müller. Pp. xi + 268. Chichester: John Wiley & Sons, 2nd ed., 2006. Price (soft cover) GBP 29.95. ISBN 978-0-470-01864-4.
http://scripts.iucr.org/cgi-bin/paper?pf0039
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-76732008-05-01doi:10.1107/S0108767308002432International Union of CrystallographyenBOOK RECEIVEDtext/htmlInorganic structural chemistry. By Ulrich Müller. Pp. xi + 268. Chichester: John Wiley & Sons, 2nd ed., 2006. Price (soft cover) GBP 29.95. ISBN 978-0-470-01864-4.text3642008-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673books received435med@iucr.org4351600-5724Crystallography Across the Sciences 2
http://scripts.iucr.org/cgi-bin/paper?me0360
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Schenk, H.2008-01-01doi:10.1107/S0108767307067098International Union of CrystallographyenPREFACEtext/htmlCrystallography Across the Sciences 2text1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673issue prefacemed@iucr.orgHigh-pressure diffraction studies of molecular organic solids. A personal view
http://scripts.iucr.org/cgi-bin/paper?sc5024
This paper discusses the trends in the experimental studies of molecular organic solids at high pressures by diffraction techniques. Crystallization of liquids, crystallization from solutions and solid-state transformations are considered. Special attention is paid to the high-pressure studies of pharmaceuticals and of biomimetics.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Boldyreva, E.V.2008-01-01doi:10.1107/S0108767307065786International Union of CrystallographyA concise review of the retrospect and prospects of high-pressure diffraction studies of organic crystals, with a special emphasis on pharmaceuticals and biomimetics.enCOMPRESSIBILITY; HYDROGEN BONDS; HYDROSTATIC PRESSURES; KINETIC CONTROL; LATTICE STRAIN; PHASE TRANSITIONS; POLYMORPHISM; SOLVENT-MEDIATED TRANSFORMATIONSThis paper discusses the trends in the experimental studies of molecular organic solids at high pressures by diffraction techniques. Crystallization of liquids, crystallization from solutions and solid-state transformations are considered. Special attention is paid to the high-pressure studies of pharmaceuticals and of biomimetics.text/htmlHigh-pressure diffraction studies of molecular organic solids. A personal viewtext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles218med@iucr.org231The MEM/Rietveld method with nano-applications – accurate charge-density studies of nano-structured materials by synchrotron-radiation powder diffraction
http://scripts.iucr.org/cgi-bin/paper?sc5018
Structural studies of materials with nano-sized spaces, called nano-structured materials, have been carried out by high-resolution powder diffraction. Our developed analytical method, which is the combination of the maximum-entropy method (MEM) and Rietveld refinement, the so-called MEM/Rietveld method, has been successfully applied to the analysis of synchrotron-radiation (SR) powder diffraction data measured at SPring-8, a third-generation SR light source. In this article, structural studies of nano-porous coordination polymers and endohedral metallofullerenes are presented with the advanced technique of SR powder experiment. The structure of the adsorbed guest molecule in the coordination polymer and encapsulated atoms in the fullerene cage are clearly revealed by the MEM charge density. The methodology of MEM/Rietveld analysis is also presented.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Takata, M.2008-01-01doi:10.1107/S010876730706521XInternational Union of CrystallographyThe role played by the MEM/Rietveld method, which is a combination of the maximum-entropy method (MEM) and Rietveld analysis, for charge-density studies is described in the structural materials science of novel nano-materials. The atoms' and molecules' charge densities inside the nano-scale spaces of fullerene cages and metal-organic coordination polymers are visualized by using synchrotron-radiation powder data.enCHARGE DENSITY; MAXIMUM-ENTROPY METHOD; METALLOFULLERENE; NANO-MATERIAL; POROUS COORDINATION POLYMERS; POWDER DIFFRACTION; SYNCHROTRON RADIATIONStructural studies of materials with nano-sized spaces, called nano-structured materials, have been carried out by high-resolution powder diffraction. Our developed analytical method, which is the combination of the maximum-entropy method (MEM) and Rietveld refinement, the so-called MEM/Rietveld method, has been successfully applied to the analysis of synchrotron-radiation (SR) powder diffraction data measured at SPring-8, a third-generation SR light source. In this article, structural studies of nano-porous coordination polymers and endohedral metallofullerenes are presented with the advanced technique of SR powder experiment. The structure of the adsorbed guest molecule in the coordination polymer and encapsulated atoms in the fullerene cage are clearly revealed by the MEM charge density. The methodology of MEM/Rietveld analysis is also presented.text/htmlThe MEM/Rietveld method with nano-applications – accurate charge-density studies of nano-structured materials by synchrotron-radiation powder diffractiontext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles232med@iucr.org245Photocrystallography
http://scripts.iucr.org/cgi-bin/paper?sc5021
This review describes the development and application of a new crystallographic technique that is starting to enable the three-dimensional structural determination of molecules in their photo-activated states. So called `photocrystallography' has wide applicability, particularly in the currently exciting area of photonics, and a discussion of this applied potential is put into context in this article. Studies are classified into four groups: photo-structural changes that are (i) irreversible; (ii) long-lived but reversible under certain conditions; (iii) transient with photo-active lifetimes of the order of microseconds; (iv) very short lived, existing at the nanosecond or even picosecond level. As photo-structural changes relative to the `ground state' can be subtle, this article necessarily concentrates on small-molecule single-crystal X-ray diffraction given that high atomic resolution is possible. That said, where it is pertinent, references are also made to related major advances in photo-induced macromolecular crystallography. The review concludes with an outlook on this new research area, including the future possibility of studying even more ephemeral, femtosecond-lived, photo-active species.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Cole, J.M.2008-01-01doi:10.1107/S0108767307065324International Union of CrystallographyA review of crystal-structure determinations of photo-induced molecular species, as derived using small-molecule single-crystal X-ray crystallography, is presented. Such species may be stable or transient, down to picoseconds, and are of substantial interest to the photonics industry.enPHOTOCRYSTALLOGRAPHYThis review describes the development and application of a new crystallographic technique that is starting to enable the three-dimensional structural determination of molecules in their photo-activated states. So called `photocrystallography' has wide applicability, particularly in the currently exciting area of photonics, and a discussion of this applied potential is put into context in this article. Studies are classified into four groups: photo-structural changes that are (i) irreversible; (ii) long-lived but reversible under certain conditions; (iii) transient with photo-active lifetimes of the order of microseconds; (iv) very short lived, existing at the nanosecond or even picosecond level. As photo-structural changes relative to the `ground state' can be subtle, this article necessarily concentrates on small-molecule single-crystal X-ray diffraction given that high atomic resolution is possible. That said, where it is pertinent, references are also made to related major advances in photo-induced macromolecular crystallography. The review concludes with an outlook on this new research area, including the future possibility of studying even more ephemeral, femtosecond-lived, photo-active species.text/htmlPhotocrystallographytext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles259med@iucr.org271Structure determination from powder diffraction data
http://scripts.iucr.org/cgi-bin/paper?sc5019
Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673David, W.I.F.Shankland, K.2008-01-01doi:10.1107/S0108767307064252International Union of CrystallographyStructure determination from powder diffraction data has developed in the past decade to the stage where the structures of many molecular materials, particularly of pharmaceutical interest, are successfully solved. The intrinsically higher symmetry and more complex topology of inorganic materials complicate their structure determination from powder diffraction data which is, as a result, less routine than its molecular counterpart. The study of small proteins from powder diffraction data alone shows great promise and the first structures have been solved. The limits of the powder diffraction technique remain to be explored, particularly if auxiliary techniques are used.enGLOBAL OPTIMIZATION; DIRECT METHODS; POWDER DIFFRACTION; STRUCTURE DETERMINATIONAdvances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.text/htmlStructure determination from powder diffraction datatext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles52med@iucr.org64An easy non-invasive X-ray diffraction method to determine the composition of Na-pyroxenes from high-density `greenstone' implements
http://scripts.iucr.org/cgi-bin/paper?sc5020
A large number of polished stone implements from Palaeolithic to Bronze Age sites of Northern Italy and Southern France are made of high-pressure (HP) metamorphic rocks (eclogite and related rocks), mainly consisting of Na-pyroxene (jadeite to omphacite) from the metamorphic belt of the Western Alps. The standard archaeometric study of prehistoric stone implements follows a procedure that is invasive, expensive and time-consuming. Since Na-pyroxenes may show a large compositional range, a thorough study of the variations affecting the dhkl values, obtained by X-ray diffraction, of three selected reflections as a function of different chemical composition was carried out, in order to determine the chemistry of Na-pyroxene isomorphic mixtures and roughly evaluate their relative amounts. These reflections (\bar221, 310, 002) are sharp, intense and sensitive to the variation of pyroxene chemical composition. Using such dhkl values measured on pyroxenes of known chemistry, a Ca-pyroxene(Di)–jadeite(Jd)–aegirine(Ae) compositional diagram was constructed, from which the composition of an unknown pyroxene can be estimated within an error of about 5%. When the size of the object is relatively small and a flat polished surface is present, the proposed analytical procedure becomes totally non-invasive. The data obtained shed light on the provenance sources of such implements and the prehistoric trade routes.urn:issn:0108-7673Giustetto, R.Chiari, G.Compagnoni, R.2008-01-01doi:10.1107/S0108767307062691International Union of CrystallographyAn innovative non-destructive method is presented for determining the chemistry of Na-pyroxene isomorphic mixtures characterizing Neolithic greenstone implements which permits their provenance and some of the prehistoric trade routes to be traced.enCLINOPYROXENE; COMPOSITIONAL GRID; JADEITE; NEOLITHIC GREENSTONE IMPLEMENTS; OMPHACITEA large number of polished stone implements from Palaeolithic to Bronze Age sites of Northern Italy and Southern France are made of high-pressure (HP) metamorphic rocks (eclogite and related rocks), mainly consisting of Na-pyroxene (jadeite to omphacite) from the metamorphic belt of the Western Alps. The standard archaeometric study of prehistoric stone implements follows a procedure that is invasive, expensive and time-consuming. Since Na-pyroxenes may show a large compositional range, a thorough study of the variations affecting the dhkl values, obtained by X-ray diffraction, of three selected reflections as a function of different chemical composition was carried out, in order to determine the chemistry of Na-pyroxene isomorphic mixtures and roughly evaluate their relative amounts. These reflections (\bar221, 310, 002) are sharp, intense and sensitive to the variation of pyroxene chemical composition. Using such dhkl values measured on pyroxenes of known chemistry, a Ca-pyroxene(Di)–jadeite(Jd)–aegirine(Ae) compositional diagram was constructed, from which the composition of an unknown pyroxene can be estimated within an error of about 5%. When the size of the object is relatively small and a flat polished surface is present, the proposed analytical procedure becomes totally non-invasive. The data obtained shed light on the provenance sources of such implements and the prehistoric trade routes.text/htmlAn easy non-invasive X-ray diffraction method to determine the composition of Na-pyroxenes from high-density `greenstone' implementstext1642008-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673feature articles161med@iucr.org168High-pressure crystallography
http://scripts.iucr.org/cgi-bin/paper?sc5016
Since the late 1950's, high-pressure structural studies have become increasingly frequent, following the inception of opposed-anvil cells, development of efficient diffractometric equipment (brighter radiation sources both in laboratories and in synchrotron facilities, highly efficient area detectors) and procedures (for crystal mounting, centring, pressure calibration, collecting and correcting data). Consequently, during the last decades, high-pressure crystallography has evolved into a powerful technique which can be routinely applied in laboratories and dedicated synchrotron and neutron facilities. The variation of pressure adds a new thermodynamic dimension to crystal-structure analyses, and extends the understanding of the solid state and materials in general. New areas of thermodynamic exploration of phase diagrams, polymorphism, transformations between different phases and cohesion forces, structure–property relations, and a deeper understanding of matter at the atomic scale in general are accessible with the high-pressure techniques in hand. A brief history, guidelines and requirements for performing high-pressure structural studies are outlined.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Katrusiak, A.2008-01-01doi:10.1107/S0108767307061181International Union of CrystallographyThe history and development of high-pressure crystallography are briefly described and examples of structural transformations in compressed compounds are given. The review is focused on the diamond-anvil cell, celebrating its 50th anniversary this year, the principles of its operation and the impact it has had on high-pressure X-ray diffraction.enDIFFRACTION; HIGH PRESSURE; HYDROGEN BONDS; PHASE TRANSITIONS; POLYMORPHISM; THERMODYNAMICSSince the late 1950's, high-pressure structural studies have become increasingly frequent, following the inception of opposed-anvil cells, development of efficient diffractometric equipment (brighter radiation sources both in laboratories and in synchrotron facilities, highly efficient area detectors) and procedures (for crystal mounting, centring, pressure calibration, collecting and correcting data). Consequently, during the last decades, high-pressure crystallography has evolved into a powerful technique which can be routinely applied in laboratories and dedicated synchrotron and neutron facilities. The variation of pressure adds a new thermodynamic dimension to crystal-structure analyses, and extends the understanding of the solid state and materials in general. New areas of thermodynamic exploration of phase diagrams, polymorphism, transformations between different phases and cohesion forces, structure–property relations, and a deeper understanding of matter at the atomic scale in general are accessible with the high-pressure techniques in hand. A brief history, guidelines and requirements for performing high-pressure structural studies are outlined.text/htmlHigh-pressure crystallographytext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles135med@iucr.org148Electron crystallography: imaging and single-crystal diffraction from powders
http://scripts.iucr.org/cgi-bin/paper?sc5017
The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Zou, X.D.Hovmöller, S.2008-01-01doi:10.1107/S0108767307060084International Union of CrystallographyDifferent techniques for structure determination from transmission electron microscopy and electron diffraction are reviewed, including three-dimensional reconstruction, the precession technique and ultrafast electron crystallography. Examples of electron-crystallography applications are given.enELECTRON CRYSTALLOGRAPHY; ELECTRON PRECESSION TECHNIQUE; THREE-DIMENSIONAL RECONSTRUCTION; ULTRAFAST ELECTRON CRYSTALLOGRAPHYThe study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.text/htmlElectron crystallography: imaging and single-crystal diffraction from powderstext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles149med@iucr.org160Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction. Addendum
http://scripts.iucr.org/cgi-bin/paper?sc5023
In the paper by Sayre [Acta Cryst. (2008), A64, 33–35], a proposal is made to use stereoscopy as a short-term means of overcoming the primarily technological hurdles involved in three-dimensional imaging of the biological cell by soft X-ray diffraction microscopy. This addendum provides a broader perspective on the techniques used by this rapidly maturing community to investigate structural problems in the biological and material sciences.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Shapiro, D.A.2008-01-01doi:10.1107/S0108767307057571International Union of CrystallographyA broad perspective on the techniques used by the coherent X-ray diffraction microscopy community is provided as an addendum to the paper by Sayre [Acta Cryst. (2008), A64, 33–35].enYEAST CELL; THREE-DIMENSIONAL IMAGING; FLASH IMAGING; SERIAL CRYSTALLOGRAPHYIn the paper by Sayre [Acta Cryst. (2008), A64, 33–35], a proposal is made to use stereoscopy as a short-term means of overcoming the primarily technological hurdles involved in three-dimensional imaging of the biological cell by soft X-ray diffraction microscopy. This addendum provides a broader perspective on the techniques used by this rapidly maturing community to investigate structural problems in the biological and material sciences.text/htmlReport on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction. Addendumtext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles36med@iucr.org37Report on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffraction
http://scripts.iucr.org/cgi-bin/paper?sc5022
Single-particle X-ray diffraction is an extension of X-ray crystallography which allows the specimen to be any small solid-state bounded object; in Shapiro et al. [Proc. Natl Acad. Sci. USA (2005), 102, 15343–15346] and Thibault et al. [Acta Cryst. (2006), A62, 248–261], the reader can find descriptions of a recent StonyBrook/Berkeley/Cornell two-dimensional imaging of a yeast cell by this technique. Our present work is aimed at extending the technique to the three-dimensional imaging of a cell. However, the usual method of doing that, namely rotating the specimen into many orientations in the X-ray beam, has not as yet given sufficiently good three-dimensional diffraction data to allow the work to go forward, the largest problem being the difficulty of preventing unwanted levels of change in the specimen through the extended exposure to a hostile environment of X-rays and, in some cases, high vacuum and/or extreme cold. The present paper discusses possible methods of dealing with this problem.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Sayre, D.2008-01-01doi:10.1107/S010876730705550XInternational Union of CrystallographyIn biocellular imaging, unwanted changes in the specimen during the longer exposures for three-dimensional data collection are making the step from two- to three-dimensional imaging difficult. Low-exposure stereoscopic three-dimensional imaging may be one answer to the problem.enYEAST CELL; THREE-DIMENSIONAL IMAGING; STEREOSCOPIC IMAGINGSingle-particle X-ray diffraction is an extension of X-ray crystallography which allows the specimen to be any small solid-state bounded object; in Shapiro et al. [Proc. Natl Acad. Sci. USA (2005), 102, 15343–15346] and Thibault et al. [Acta Cryst. (2006), A62, 248–261], the reader can find descriptions of a recent StonyBrook/Berkeley/Cornell two-dimensional imaging of a yeast cell by this technique. Our present work is aimed at extending the technique to the three-dimensional imaging of a cell. However, the usual method of doing that, namely rotating the specimen into many orientations in the X-ray beam, has not as yet given sufficiently good three-dimensional diffraction data to allow the work to go forward, the largest problem being the difficulty of preventing unwanted levels of change in the specimen through the extended exposure to a hostile environment of X-rays and, in some cases, high vacuum and/or extreme cold. The present paper discusses possible methods of dealing with this problem.text/htmlReport on a project on three-dimensional imaging of the biological cell by single-particle X-ray diffractiontext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles33med@iucr.org35Stability of ferroic phases in the highly piezoelectric Pb(ZrxTi1−x)O3 ceramics
http://scripts.iucr.org/cgi-bin/paper?sc5013
The morphotropic phase boundary in the phase diagram of the technologically important Pb(ZrxTi1−x)O3 (PZT) ceramics has been traditionally believed to separate ferroelectric tetragonal and rhombohedral phase regions. This old picture has come under close scrutiny during the last eight years following the discovery of new monoclinic phases in the Cm and Cc space groups. This article presents a brief overview of these discoveries in which the use of multiple diffraction probes (X-ray, electron, neutron diffraction) in conjunction with physical property measurements has played a crucial role. A new phase diagram of PZT showing the stability fields of these structures below room temperature is also presented.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Pandey, D.Singh, A.K.Baik, S.2008-01-01doi:10.1107/S0108767307055511International Union of CrystallographyAn overview of the recent discoveries of the monoclinic phases in the Cm and Cc space groups and their stability fields in the Pb(ZrxTi1−x)O3 phase diagram is presented.enFERROIC PHASES; PIEZOELECTRIC PB(ZRXTI1-X)O3 CERAMICS (PZT)The morphotropic phase boundary in the phase diagram of the technologically important Pb(ZrxTi1−x)O3 (PZT) ceramics has been traditionally believed to separate ferroelectric tetragonal and rhombohedral phase regions. This old picture has come under close scrutiny during the last eight years following the discovery of new monoclinic phases in the Cm and Cc space groups. This article presents a brief overview of these discoveries in which the use of multiple diffraction probes (X-ray, electron, neutron diffraction) in conjunction with physical property measurements has played a crucial role. A new phase diagram of PZT showing the stability fields of these structures below room temperature is also presented.text/htmlStability of ferroic phases in the highly piezoelectric Pb(ZrxTi1−x)O3 ceramicstext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles192med@iucr.org203Theories and techniques of crystal structure determination. By Uri Shmueli, Pp. 269. Oxford: Oxford University Press, 2007. Price GBP 32.50. ISBN 978-0-19-921350-4.
http://scripts.iucr.org/cgi-bin/paper?pf0061
Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Rutherford, J.S.2008-03-01doi:10.1107/S0108767308002419International Union of CrystallographyenBOOK REVIEWtext/htmlTheories and techniques of crystal structure determination. By Uri Shmueli, Pp. 269. Oxford: Oxford University Press, 2007. Price GBP 32.50. ISBN 978-0-19-921350-4.text2642008-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673book reviews348med@iucr.org3481600-5724On wine, chirality and crystallography
http://scripts.iucr.org/cgi-bin/paper?sc5012
As the first centennial of X-ray diffraction is inevitably drawing closer, it is tempting to reflect on the impact that this fascinating discipline has had on natural sciences and how it has changed the world we live in. Also, next year is the 160th anniversary of the fateful April afternoon when Louis Pasteur separated d- from l-tartrate crystals, an event that many science historians recognize as the birth of stereochemistry, and the first step that the barely nascent field of crystallography took on the road to elucidate a fundamental phenomenon of chemistry and biology – chirality. Many great minds – Pasteur, Van 't Hoff, Fischer, Lord Kelvin, the Braggs, Astbury and Bijvoet, to mention just a few – contributed along the way. But one central inanimate character was there at all times – an inconspicuous somewhat obscure organic compound found in wine: tartaric acid. This is the story of its contribution to science.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Derewenda, Z.S.2008-01-01doi:10.1107/S0108767307054293International Union of CrystallographyHow tartaric acid, an inconspicuous organic compound found in wine, made a pivotal contribution to structural chemistry and biology.enCHIRALITY; TARTARIC ACIDAs the first centennial of X-ray diffraction is inevitably drawing closer, it is tempting to reflect on the impact that this fascinating discipline has had on natural sciences and how it has changed the world we live in. Also, next year is the 160th anniversary of the fateful April afternoon when Louis Pasteur separated d- from l-tartrate crystals, an event that many science historians recognize as the birth of stereochemistry, and the first step that the barely nascent field of crystallography took on the road to elucidate a fundamental phenomenon of chemistry and biology – chirality. Many great minds – Pasteur, Van 't Hoff, Fischer, Lord Kelvin, the Braggs, Astbury and Bijvoet, to mention just a few – contributed along the way. But one central inanimate character was there at all times – an inconspicuous somewhat obscure organic compound found in wine: tartaric acid. This is the story of its contribution to science.text/htmlOn wine, chirality and crystallographytext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles246med@iucr.org258The search for a structural basis for therapeutic intervention against the SARS coronavirus
http://scripts.iucr.org/cgi-bin/paper?sc5014
The 2003 outbreak of severe acute respiratory syndrome (SARS), caused by a previously unknown coronavirus called SARS-CoV, had profound social and economic impacts worldwide. Since then, structure–function studies of SARS-CoV proteins have provided a wealth of information that increases our understanding of the underlying mechanisms of SARS. While no effective therapy is currently available, considerable efforts have been made to develop vaccines and drugs to prevent SARS-CoV infection. In this review, some of the notable achievements made by SARS structural biology projects worldwide are examined and strategies for therapeutic intervention are discussed based on available SARS-CoV protein structures. To date, 12 structures have been determined by X-ray crystallography or NMR from the 28 proteins encoded by SARS-CoV. One key protein, the SARS-CoV main protease (Mpro), has been the focus of considerable structure-based drug discovery efforts. This article highlights the importance of structural biology and shows that structures for drug design can be rapidly determined in the event of an emerging infectious disease.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Bartlam, M.Xue, X.Rao, Z.2008-01-01doi:10.1107/S0108767307054426International Union of CrystallographyThe severe acute respiratory syndrome (SARS) coronavirus outbreak in 2003 had profound social and economic impacts worldwide. This review highlights the importance of structural biology and shows that structures for drug design can be rapidly determined in the event of an emerging infectious disease.enDRUG DESIGN; SARS CORONAVIRUS; SARS-COVThe 2003 outbreak of severe acute respiratory syndrome (SARS), caused by a previously unknown coronavirus called SARS-CoV, had profound social and economic impacts worldwide. Since then, structure–function studies of SARS-CoV proteins have provided a wealth of information that increases our understanding of the underlying mechanisms of SARS. While no effective therapy is currently available, considerable efforts have been made to develop vaccines and drugs to prevent SARS-CoV infection. In this review, some of the notable achievements made by SARS structural biology projects worldwide are examined and strategies for therapeutic intervention are discussed based on available SARS-CoV protein structures. To date, 12 structures have been determined by X-ray crystallography or NMR from the 28 proteins encoded by SARS-CoV. One key protein, the SARS-CoV main protease (Mpro), has been the focus of considerable structure-based drug discovery efforts. This article highlights the importance of structural biology and shows that structures for drug design can be rapidly determined in the event of an emerging infectious disease.text/htmlThe search for a structural basis for therapeutic intervention against the SARS coronavirustext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles204med@iucr.org213Busting out of crystallography's Sisyphean prison: from pencil and paper to structure solving at the press of a button: past, present and future of crystallographic software development, maintenance and distribution
http://scripts.iucr.org/cgi-bin/paper?sc5015
The history of crystallographic computing and use of crystallographic software is one which traces the escape from the drudgery of manual human calculations to a world where the user delegates most of the travail to electronic computers. In practice, this involves practising crystallographers communicating their thoughts to the crystallographic program authors, in the hope that new procedures will be implemented within their software. Against this background, the development of small-molecule single-crystal and powder diffraction software is traced. Starting with the analogue machines and the use of Hollerith tabulators of the late 1930's, it is shown that computing developments have been science led, with new technologies being harnessed to solve pressing crystallographic problems. The development of software is also traced, with a final caution that few of the computations now performed daily are really understood by the program users. Unless a sufficient body of people continues to dismantle and re-build programs, the knowledge encoded in the old programs will become as inaccessible as the knowledge of how to build the Great Pyramid at Giza.urn:issn:0108-7673Cranswick, L.M.D.2008-01-01doi:10.1107/S0108767307051355International Union of CrystallographyThe history of crystallographic computing and use of crystallographic software is one which traces the escape from the drudgery of manual human calculations to a world where the user delegates most of the travail to electronic computers. This review traces the development of small-molecule single-crystal and powder diffraction hardware, starting with the use of Hollerith tabulators of the late 1930's through to today's use of high-performance personal computers. It also emphasizes that the main challenge for current and future crystallography computing is not that of hardware development, or even specific scientific challenges, but rather in maintaining a critical mass of human expertise with which these computational challenges can be undertaken.enBEEVERS; COMRIE; ECKERT; HISTORY; HOLLERITH; PAULING; POWDER DIFFRACTION; SINGLE CRYSTAL; SOFTWARE; TEACHINGThe history of crystallographic computing and use of crystallographic software is one which traces the escape from the drudgery of manual human calculations to a world where the user delegates most of the travail to electronic computers. In practice, this involves practising crystallographers communicating their thoughts to the crystallographic program authors, in the hope that new procedures will be implemented within their software. Against this background, the development of small-molecule single-crystal and powder diffraction software is traced. Starting with the analogue machines and the use of Hollerith tabulators of the late 1930's, it is shown that computing developments have been science led, with new technologies being harnessed to solve pressing crystallographic problems. The development of software is also traced, with a final caution that few of the computations now performed daily are really understood by the program users. Unless a sufficient body of people continues to dismantle and re-build programs, the knowledge encoded in the old programs will become as inaccessible as the knowledge of how to build the Great Pyramid at Giza.text/htmlBusting out of crystallography's Sisyphean prison: from pencil and paper to structure solving at the press of a button: past, present and future of crystallographic software development, maintenance and distributiontext1642008-01-01Acta Crystallographica Section A: Foundations of Crystallography0108-7673feature articles65med@iucr.org87Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS
http://scripts.iucr.org/cgi-bin/paper?sc5002
Methods of contrast variation are tools that are essential in macromolecular structure research. Anomalous dispersion of X-ray diffraction is widely used in protein crystallography. Recent attempts to extend this method to native resonant labels like sulfur and phosphorus are promising. Substitution of hydrogen isotopes is central to biological applications of neutron scattering. Proton spin polarization considerably enhances an existing contrast prepared by isotopic substitution. Concepts and methods of nuclear magnetic resonance (NMR) become an important ingredient in neutron scattering from dynamically polarized targets.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Stuhrmann, H.B.2008-01-01doi:10.1107/S0108767307046569International Union of CrystallographyOriginally conceived for protein crystallography, contrast variation has become a favourite tool of small-angle scattering. Recent developments in contrast variation are reviewed.enANOMALOUS DISPERSION; DYNAMIC NUCLEAR POLARIZATION; ISOTOPIC SUBSTITUTION; UNIQUENESSMethods of contrast variation are tools that are essential in macromolecular structure research. Anomalous dispersion of X-ray diffraction is widely used in protein crystallography. Recent attempts to extend this method to native resonant labels like sulfur and phosphorus are promising. Substitution of hydrogen isotopes is central to biological applications of neutron scattering. Proton spin polarization considerably enhances an existing contrast prepared by isotopic substitution. Concepts and methods of nuclear magnetic resonance (NMR) become an important ingredient in neutron scattering from dynamically polarized targets.text/htmlSmall-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANStext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles181med@iucr.org191The charge flipping algorithm
http://scripts.iucr.org/cgi-bin/paper?sc5009
This paper summarizes the current state of charge flipping, a recently developed algorithm of ab initio structure determination. Its operation is based on the perturbation of large plateaus of low electron density but not directly on atomicity. Such a working principle radically differs from that of classical direct methods and offers complementary applications. The list of successful structure-solution cases includes periodic and aperiodic crystals using single-crystal and powder diffraction data measured with X-ray and neutron radiation. Apart from counting applications, the paper mainly deals with algorithmic issues: it describes and compares new variants of the iteration scheme, helps to identify and improve solutions, discusses the required data and the use of known information. Finally, it tries to foretell the future of such an alternative among well established direct methods.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Oszlányi, G.Sütő, A.2008-01-01doi:10.1107/S0108767307046028International Union of CrystallographyThe current state of the charge flipping algorithm is reviewed.enAB INITIO STRUCTURE DETERMINATION; CHARGE FLIPPING ALGORITHMThis paper summarizes the current state of charge flipping, a recently developed algorithm of ab initio structure determination. Its operation is based on the perturbation of large plateaus of low electron density but not directly on atomicity. Such a working principle radically differs from that of classical direct methods and offers complementary applications. The list of successful structure-solution cases includes periodic and aperiodic crystals using single-crystal and powder diffraction data measured with X-ray and neutron radiation. Apart from counting applications, the paper mainly deals with algorithmic issues: it describes and compares new variants of the iteration scheme, helps to identify and improve solutions, discusses the required data and the use of known information. Finally, it tries to foretell the future of such an alternative among well established direct methods.text/htmlThe charge flipping algorithmtext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles123med@iucr.org134Crystallographic publishing in the electronic age
http://scripts.iucr.org/cgi-bin/paper?sc5008
The journals of the International Union of Crystallography have grown in size and number over the past 60 years to match developments in scientific practice and technique. High quality of publication has always been at the forefront of editorial policy and ways in which this has been achieved are described. In particular, the development of standard exchange and archive formats for crystallographic data has allowed the editorial office to conduct automated analyses of structural data supporting articles submitted for publication and these analyses assist the scientific editors in careful and critical peer review. The new information technologies of the Internet age have allowed the IUCr journals to flourish and to provide a wide range of powerful services to authors, editors and readers alike. The integration of literature and supporting structural data is of particular importance. The new technologies have also brought fresh economic and cultural challenges, and offer completely new opportunities to disseminate the results of scientific research. The journals continue to respond to these challenges and take advantage of new opportunities in innovative ways.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Strickland, P.R.McMahon, B.2008-01-01doi:10.1107/S0108767307045801International Union of CrystallographyThe journal publishing activities of the IUCr over the past 60 years are described, together with the new technological, economic and cultural challenges faced by the journals. Particular emphasis is placed on the role of innovative publishing technologies in ensuring the quality of the published information and in providing effective access to the data underpinning the scientific results.enCRYSTALLOGRAPHIC PUBLISHING; IUCR JOURNALSThe journals of the International Union of Crystallography have grown in size and number over the past 60 years to match developments in scientific practice and technique. High quality of publication has always been at the forefront of editorial policy and ways in which this has been achieved are described. In particular, the development of standard exchange and archive formats for crystallographic data has allowed the editorial office to conduct automated analyses of structural data supporting articles submitted for publication and these analyses assist the scientific editors in careful and critical peer review. The new information technologies of the Internet age have allowed the IUCr journals to flourish and to provide a wide range of powerful services to authors, editors and readers alike. The integration of literature and supporting structural data is of particular importance. The new technologies have also brought fresh economic and cultural challenges, and offer completely new opportunities to disseminate the results of scientific research. The journals continue to respond to these challenges and take advantage of new opportunities in innovative ways.text/htmlCrystallographic publishing in the electronic agetext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles38med@iucr.org51Does mathematical crystallography still have a role in the XXI century?
http://scripts.iucr.org/cgi-bin/paper?sc5006
Mathematical crystallography is the branch of crystallography dealing specifically with the fundamental properties of symmetry and periodicity of crystals, topological properties of crystal structures, twins, modular and modulated structures, polytypes and OD structures, as well as the symmetry aspects of phase transitions and physical properties of crystals. Mathematical crystallography has had its most evident success with the development of the theory of space groups at the end of the XIX century; since then, it has greatly enlarged its applications, but crystallographers are not always familiar with the developments that followed, partly because the applications sometimes require some additional background that the structural crystallographer does not always possess (as is the case, for example, in graph theory). The knowledge offered by mathematical crystallography is at present only partly mirrored in International Tables for Crystallography and is sometimes still enshrined in more specialist texts and publications. To cover this communication gap is one of the tasks of the IUCr Commission on Mathematical and Theoretical Crystallography (MaThCryst).Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2008-01-01doi:10.1107/S0108767307044625International Union of CrystallographyA survey of some of the main topics of mathematical crystallography is presented, together with the challenges for future developments.enGRAPH THEORY; MATHEMATICAL CRYSTALLOGRAPHY; OD STRUCTURES; POLYTYPES; SYMMETRY; THEORETICAL CRYSTALLOGRAPHY; TOPOLOGY; TWINSMathematical crystallography is the branch of crystallography dealing specifically with the fundamental properties of symmetry and periodicity of crystals, topological properties of crystal structures, twins, modular and modulated structures, polytypes and OD structures, as well as the symmetry aspects of phase transitions and physical properties of crystals. Mathematical crystallography has had its most evident success with the development of the theory of space groups at the end of the XIX century; since then, it has greatly enlarged its applications, but crystallographers are not always familiar with the developments that followed, partly because the applications sometimes require some additional background that the structural crystallographer does not always possess (as is the case, for example, in graph theory). The knowledge offered by mathematical crystallography is at present only partly mirrored in International Tables for Crystallography and is sometimes still enshrined in more specialist texts and publications. To cover this communication gap is one of the tasks of the IUCr Commission on Mathematical and Theoretical Crystallography (MaThCryst).text/htmlDoes mathematical crystallography still have a role in the XXI century?text1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles96med@iucr.org111A short history of SHELX
http://scripts.iucr.org/cgi-bin/paper?sc5010
An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Sheldrick, G.M.2008-01-01doi:10.1107/S0108767307043930International Union of CrystallographyThe SHELX programs for crystal structure determination are reviewed by their author.enCOMPUTER PROGRAMS; CRYSTAL STRUCTURE DETERMINATION; PHASING; SHELX; STRUCTURE REFINEMENTAn account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.text/htmlA short history of SHELXtext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles112med@iucr.org122Powder crystallography on macromolecules
http://scripts.iucr.org/cgi-bin/paper?sc5011
Following the seminal work of Von Dreele, powder X-ray diffraction studies on proteins are being established as a valuable complementary technique to single-crystal measurements. A wide range of small proteins have been found to give synchrotron powder diffraction profiles where the peak widths are essentially limited only by the instrumental resolution. The rich information contained in these profiles, combined with developments in data analysis, has stimulated research and development to apply the powder technique to microcrystalline protein samples. In the present work, progress in using powder diffraction for macromolecular crystallography is reported.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Margiolaki, I.Wright, J.P.2008-01-01doi:10.1107/S0108767307043735International Union of CrystallographyThe last 10 years have seen a revolution in powder crystallography; macromolecules can now be studied using powder samples. When large single crystals are not available then crystallographic information may be obtained from a polycrystalline powder instead.enPOWDER DIFFRACTION; PROTEIN CRYSTALLOGRAPHY; SYNCHROTRON RADIATIONFollowing the seminal work of Von Dreele, powder X-ray diffraction studies on proteins are being established as a valuable complementary technique to single-crystal measurements. A wide range of small proteins have been found to give synchrotron powder diffraction profiles where the peak widths are essentially limited only by the instrumental resolution. The rich information contained in these profiles, combined with developments in data analysis, has stimulated research and development to apply the powder technique to microcrystalline protein samples. In the present work, progress in using powder diffraction for macromolecular crystallography is reported.text/htmlPowder crystallography on macromoleculestext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles169med@iucr.org180Neutron protein crystallography: beyond the folding structure of biological macromolecules
http://scripts.iucr.org/cgi-bin/paper?sc5005
Neutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5–2.5 Å. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3 configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Niimura, N.Bau, R.2008-01-01doi:10.1107/S0108767307043498International Union of CrystallographySeveral results from neutron protein crystallography relating H-atom positions and hydration patterns in proteins and oligonucleotides are reviewed.enBIOLOGICAL MACROMOLECULES; FOLDING STRUCTURE; NEUTRON PROTEIN CRYSTALLOGRAPHYNeutron diffraction provides an experimental method of directly locating H atoms in proteins, a technique complementary to ultra-high-resolution X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the USA, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5–2.5 Å. Results relating to H-atom positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, the role of H atoms in enzymatic activity, CH3 configuration, H/D exchange in proteins and oligonucleotides, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals and a database of hydrogen and hydration in proteins, are described.text/htmlNeutron protein crystallography: beyond the folding structure of biological macromoleculestext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles12med@iucr.org22The interpretation and analysis of diffuse scattering using Monte Carlo simulation methods
http://scripts.iucr.org/cgi-bin/paper?sc5007
Studies of diffuse scattering had a prominent place in the first issue of Acta Crystallographica 60 years ago at a time when conventional crystallography (determination of the average structure from Bragg peaks) was in its infancy. Since that time, conventional crystallography has developed enormously while diffuse-scattering analysis has seemingly lagged well behind. The paper highlights some of the extra difficulties involved in the measurement, interpretation and analysis of diffuse scattering and plots the progress that has been made. With the advent of the latest X-ray and neutron sources, area detectors and the ever-increasing power of computers, most disorder problems are now tractable. Two recent contrasting examples are described which highlight what can be achieved by current methods.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Welberry, T.R.Goossens, D.J.2008-01-01doi:10.1107/S0108767307041918International Union of CrystallographyThe paper highlights some of the extra difficulties involved in the measurement, interpretation and analysis of diffuse scattering relative to the methods of conventional crystallography and plots the progress that has been made in the lifetime of Acta Crystallographica. With the advent of the latest X-ray and neutron sources, area detectors and the ever-increasing power of computers, most diffuse scattering and disorder problems are now tractable.enDIFFUSE SCATTERING; MONTE CARLO METHODSStudies of diffuse scattering had a prominent place in the first issue of Acta Crystallographica 60 years ago at a time when conventional crystallography (determination of the average structure from Bragg peaks) was in its infancy. Since that time, conventional crystallography has developed enormously while diffuse-scattering analysis has seemingly lagged well behind. The paper highlights some of the extra difficulties involved in the measurement, interpretation and analysis of diffuse scattering and plots the progress that has been made. With the advent of the latest X-ray and neutron sources, area detectors and the ever-increasing power of computers, most disorder problems are now tractable. Two recent contrasting examples are described which highlight what can be achieved by current methods.text/htmlThe interpretation and analysis of diffuse scattering using Monte Carlo simulation methodstext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles23med@iucr.org32Complete online set of International tables for crystallography, Vols. A–G. Edited by H. Fuess, Th. Hahn, H. Wondratschek, U. Müller, U. Shmueli, E. Prince, A. Authier, V. Kopský, D. B. Litvin, M. G. Rossmann, E. Arnold, S. Hall and B. McMahon. Springer, jointly published with the IUCr, 2007. Price for online access USD 2080.00. eISBN: 978-1-4020-5259-0, doi: 10.1107/97809553602060000001, http://it.iucr.org.
http://scripts.iucr.org/cgi-bin/paper?pf0062
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Paufler, P.2007-11-01doi:10.1107/S0108767307041207International Union of CrystallographyenBOOK REVIEWtext/htmlComplete online set of International tables for crystallography, Vols. A–G. Edited by H. Fuess, Th. Hahn, H. Wondratschek, U. Müller, U. Shmueli, E. Prince, A. Authier, V. Kopský, D. B. Litvin, M. G. Rossmann, E. Arnold, S. Hall and B. McMahon. Springer, jointly published with the IUCr, 2007. Price for online access USD 2080.00. eISBN: 978-1-4020-5259-0, doi: 10.1107/97809553602060000001, http://it.iucr.org.text6632007-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673book reviews483med@iucr.org4831600-5724Nexus, crystallographic computing all around the world
http://scripts.iucr.org/cgi-bin/paper?sc5001
Crystallographic Nexus CD-ROMs, containing a range of free crystallographic software for single-crystal and powder diffraction available on the Internet, have been distributed on request since 1996. The free CD is made in the form of a `virtual Internet' with the main intent of benefiting crystallographers with inadequate Internet access. The IUCr funds an annual/biennial update which is distributed to known previous recipients. Feedback from current recipients indicates the CD is still useful. The most current IUCr-funded CD is being produced by the CCP14 project at University College London and The Royal Institution UK for distribution to the ECM 2007 and AsCA 2007 conferences.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Cranswick, L.M.D.Bisson, W.Cockcroft, J.K.2008-01-01doi:10.1107/S0108767307040573International Union of CrystallographyCrystallographic Nexus CD-ROMs, containing a range of free crystallographic software for single-crystal and powder diffraction available on the Internet, have been distributed free on request since 1996. The free CD is made in the form of a `virtual Internet' with the main intent of benefiting crystallographers with inadequate Internet access.enCD-ROM; CRYSTALLOGRAPHIC SOFTWARE; INTERNET; POWDER DIFFRACTION; SINGLE CRYSTALCrystallographic Nexus CD-ROMs, containing a range of free crystallographic software for single-crystal and powder diffraction available on the Internet, have been distributed on request since 1996. The free CD is made in the form of a `virtual Internet' with the main intent of benefiting crystallographers with inadequate Internet access. The IUCr funds an annual/biennial update which is distributed to known previous recipients. Feedback from current recipients indicates the CD is still useful. The most current IUCr-funded CD is being produced by the CCP14 project at University College London and The Royal Institution UK for distribution to the ECM 2007 and AsCA 2007 conferences.text/htmlNexus, crystallographic computing all around the worldtext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles214med@iucr.org217Durward William John Cruickshank (1924–2007)
http://scripts.iucr.org/cgi-bin/paper?es0361
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Helliwell, J.R.Abrahams, S.C.2007-09-01doi:10.1107/S0108767307039062International Union of CrystallographyenOBITUARIEStext/htmlDurward William John Cruickshank (1924–2007)text5632007-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673obituaries375med@iucr.org3791600-5724Fascinating quasicrystals
http://scripts.iucr.org/cgi-bin/paper?sc5003
It took Dan Shechtman more than two years to get his discovery of an Al–Mn phase with icosahedral diffraction symmetry and sharp Bragg reflections published. A paradigm shift had to take place before this novel ordering state of matter – seemingly contradicting crystallographic laws – could be accepted. Today, more than 25 years later, the existence of quasicrystals is beyond doubt. However, not everything is settled yet. All the factors governing formation, growth, stability and structure of quasicrystals are still not fully understood, nor is it resolved whether their structures are strictly or only on average quasiperiodic, and it is still an open question why only quasicrystals with 5-, 8-, 10- and 12-fold rotational symmetry have been experimentally observed so far. These points will be addressed in this review article.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Steurer, W.Deloudi, S.2008-01-01doi:10.1107/S0108767307038627International Union of CrystallographyThe state of the art of structure research on quasicrystals is reviewed. Some questions concerning formation, growth and stability are addressed.enDECAGONAL PHASES; ICOSAHEDRAL PHASES; N-DIMENSIONAL APPROACH; PHOTONIC QUASICRYSTALS; QUASICRYSTALSIt took Dan Shechtman more than two years to get his discovery of an Al–Mn phase with icosahedral diffraction symmetry and sharp Bragg reflections published. A paradigm shift had to take place before this novel ordering state of matter – seemingly contradicting crystallographic laws – could be accepted. Today, more than 25 years later, the existence of quasicrystals is beyond doubt. However, not everything is settled yet. All the factors governing formation, growth, stability and structure of quasicrystals are still not fully understood, nor is it resolved whether their structures are strictly or only on average quasiperiodic, and it is still an open question why only quasicrystals with 5-, 8-, 10- and 12-fold rotational symmetry have been experimentally observed so far. These points will be addressed in this review article.text/htmlFascinating quasicrystalstext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles1med@iucr.org11The introduction of structure types into the Inorganic Crystal Structure Database ICSD
http://scripts.iucr.org/cgi-bin/paper?sh0188
Both the approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported. Extending earlier work, an hierarchical set of criteria for the separation of isopointal structures into isoconfigurational structure types is used. It is shown how these criteria, which include the space group (number), Wyckoff sequence and Pearson symbol, c/a ratio, β ranges, ANX formulae and, in certain cases, the necessary elements and forbidden elements, may be used to uniquely identify the representative structure types of the compounds contained in the ICSD database.Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Allmann, R.Hinek, R.2007-09-01doi:10.1107/S0108767307038081International Union of CrystallographyThe approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported.enINORGANIC CRYSTAL STRUCTURE DATABASE; ICSD; STRUCTURE TYPESBoth the approach used and the progress made in the assignment of structure types to the crystal structures contained in the ICSD database are reported. Extending earlier work, an hierarchical set of criteria for the separation of isopointal structures into isoconfigurational structure types is used. It is shown how these criteria, which include the space group (number), Wyckoff sequence and Pearson symbol, c/a ratio, β ranges, ANX formulae and, in certain cases, the necessary elements and forbidden elements, may be used to uniquely identify the representative structure types of the compounds contained in the ICSD database.text/htmlThe introduction of structure types into the Inorganic Crystal Structure Database ICSDtext5632007-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673research papers412med@iucr.org4171600-5724The Protein Data Bank: a historical perspective
http://scripts.iucr.org/cgi-bin/paper?sc5004
The Protein Data Bank began as a grassroots effort in 1971. It has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40000 entries. The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource.Copyright (c) 2008 International Union of Crystallographyurn:issn:0108-7673Berman, H.M.2008-01-01doi:10.1107/S0108767307035623International Union of CrystallographySince 1971, the Protein Data Bank archive of biological macromolecules has been a community-driven resource for science and education worldwide.enDATABASES; HISTORY OF PDB; NUCLEIC ACIDS; POLICY RELATIVE TO PDB; PROTEINSThe Protein Data Bank began as a grassroots effort in 1971. It has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40000 entries. The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource.text/htmlThe Protein Data Bank: a historical perspectivetext1642008-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2008 International Union of Crystallography0108-7673feature articles88med@iucr.org95Structure and chemistry of crystalline solids. By B. Douglas and S.-M. Ho. Pp. X + 346. New York: Springer 2006. Price (hardcover) EUR 106.95. ISBN 978-0-387-26147-8.
http://scripts.iucr.org/cgi-bin/paper?pf0051
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Röhr, C.2007-07-01doi:10.1107/S0108767307027250International Union of CrystallographyenBOOK REVIEWtext/htmlStructure and chemistry of crystalline solids. By B. Douglas and S.-M. Ho. Pp. X + 346. New York: Springer 2006. Price (hardcover) EUR 106.95. ISBN 978-0-387-26147-8.text4632007-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673book reviews374med@iucr.org3741600-5724The chemical bond in inorganic chemistry. The bond valence model. By I. David Brown. Pp. 278. Oxford: Oxford University Press, 2006. Price (paperback) GBP 35.00. ISBN 0-19-929881-5.
http://scripts.iucr.org/cgi-bin/paper?pf0034
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Paufler, P.P.2007-07-01doi:10.1107/S0108767307021344International Union of CrystallographyenBOOK RECEIVEDtext/htmlThe chemical bond in inorganic chemistry. The bond valence model. By I. David Brown. Pp. 278. Oxford: Oxford University Press, 2006. Price (paperback) GBP 35.00. ISBN 0-19-929881-5.text4632007-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673books received374med@iucr.org3741600-5724Personal X-ray reflections. By U. W. Arndt. Pp. 177. Twickenham: Athena Press, 2006. Price GBP 6.99, USD 11.95. ISBN 1-84401-694-3.
http://scripts.iucr.org/cgi-bin/paper?pf0948
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Helliwell, J.R.2007-09-01doi:10.1107/S0108767307019125International Union of CrystallographyenBOOK REVIEWtext/htmlPersonal X-ray reflections. By U. W. Arndt. Pp. 177. Twickenham: Athena Press, 2006. Price GBP 6.99, USD 11.95. ISBN 1-84401-694-3.text5632007-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673book reviews439med@iucr.org4401600-5724Diffraction with a coherent X-ray beam: dynamics and imaging. Erratum
http://scripts.iucr.org/cgi-bin/paper?sh9049
In the paper by Livet [Acta Cryst. (2007), A63, 63–87], equation (15) is incorrect. The correct equation is \beta(z) = \left\{\textstyle\sum\limits_{n = 0}^{\infty} (-1){}^n 2^{2n+2}z^{2n}/[(2n+1)(2n+2){}^2(2n+1)!]\right\}^2.\eqno(15)Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Livet, F.2007-05-01doi:10.1107/S0108767307016248International Union of CrystallographyErratum to Livet [Acta Cryst. (2007), A63, 63–87].enCOHERENT X-RAY BEAMS; DYNAMICS OF FLUCTUATIONS; LENSLESS IMAGING; SMALL-ANGLE SET-UPSIn the paper by Livet [Acta Cryst. (2007), A63, 63–87], equation (15) is incorrect. The correct equation is \beta(z) = \left\{\textstyle\sum\limits_{n = 0}^{\infty} (-1){}^n 2^{2n+2}z^{2n}/[(2n+1)(2n+2){}^2(2n+1)!]\right\}^2.\eqno(15)text/htmlDiffraction with a coherent X-ray beam: dynamics and imaging. Erratumtext3632007-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673addenda and errata287med@iucr.org2871600-5724Handbook of X-ray data. By G. Zschornack. Pp. IX + 967. Berlin: Springer-Verlag, 2007. Price (hardback) EUR 213.95. ISBN 978-3-540-28618-9.
http://scripts.iucr.org/cgi-bin/paper?pf0045
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Paufler, P.2007-05-01doi:10.1107/S0108767307011506International Union of CrystallographyenBOOK RECEIVEDtext/htmlHandbook of X-ray data. By G. Zschornack. Pp. IX + 967. Berlin: Springer-Verlag, 2007. Price (hardback) EUR 213.95. ISBN 978-3-540-28618-9.text3632007-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673books received288med@iucr.org2881600-5724Response to Spackman's comment on On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model
http://scripts.iucr.org/cgi-bin/paper?sh0187
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Volkov, A.Coppens, P.2007-03-01doi:10.1107/S0108767307002620International Union of CrystallographyResponse to Spackman's comment on Volkov, King, Coppens & Farrugia [Acta Cryst. (2006), A62, 400–408].entext/htmlResponse to Spackman's comment on On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom modeltext2632007-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673letters to the editor201med@iucr.org2031600-5724Comment on On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model by Volkov, King, Coppens & Farrugia (2006)
http://scripts.iucr.org/cgi-bin/paper?sh5054
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Spackman, M.A.2007-03-01doi:10.1107/S0108767307001298International Union of CrystallographyComment on Volkov, King, Coppens & Farrugia [Acta Cryst. (2006), A62, 400–408].enASPHERICAL PSEUDOATOM MODEL; ELECTRIC FIELD; ELECTRIC FIELD GRADIENT; ELECTROSTATIC POTENTIALtext/htmlComment on On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model by Volkov, King, Coppens & Farrugia (2006)text2632007-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673letters to the editor198med@iucr.org2001600-5724Coherent coexistence of nanodiamonds and carbon onions in icosahedral core-shell particles
http://scripts.iucr.org/cgi-bin/paper?dm5003
The general approach for describing and designing complex hierarchical icosahedral structures is discussed. Structural models of icosahedral carbon nanoparticles in which the local arrangement of atoms is virtually identical to that in diamond are derived. It is shown that icosahedral diamond-like particles can be transformed into onion-like shell structures (and vice versa) by the consecutive smoothing (puckering) of atomic networks without disturbance of their topological integrity. The possibility of coherent coexistence of icosahedral diamond-like core with onion shells is shown.Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Shevchenko, V.Ya.Madison, A.E.Mackay, A.L.2007-03-01doi:10.1107/S0108767307002723International Union of CrystallographyIn icosahedral carbon nanoparticles, the diamond-like core can undergo a reversible topological transition into and coexist coherently with the onion shells.enCARBON ONION; COHERENT COEXISTENCE; NANODIAMONDThe general approach for describing and designing complex hierarchical icosahedral structures is discussed. Structural models of icosahedral carbon nanoparticles in which the local arrangement of atoms is virtually identical to that in diamond are derived. It is shown that icosahedral diamond-like particles can be transformed into onion-like shell structures (and vice versa) by the consecutive smoothing (puckering) of atomic networks without disturbance of their topological integrity. The possibility of coherent coexistence of icosahedral diamond-like core with onion shells is shown.text/htmlCoherent coexistence of nanodiamonds and carbon onions in icosahedral core-shell particlestext2632007-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673research papers172med@iucr.org1761600-5724Diffraction with a coherent X-ray beam: dynamics and imaging
http://scripts.iucr.org/cgi-bin/paper?sh5049
Methods for carrying out coherent X-ray scattering experiments are reviewed. The brilliance of the available synchrotron sources, the characteristics of the existing optics, the various ways of obtaining a beam of controlled coherence properties and the detectors used are summarized. Applications in the study of the dynamics of speckle patterns are described. In the case of soft condensed matter, the movement of inclusions like fillers in polymers or colloidal particles can be observed and these can reflect polymer or liquid-crystal fluctuations. In hard condensed-matter problems, like phase transitions, charge-density waves or phasons in quasicrystals, the study of speckle fluctuations provides new time-resolved methods. In the domain of lensless imaging, the coherent beam gives the modulus of the sample Fourier transform. If oversampling conditions are fulfilled, the phase can be obtained and the image in the direct space can be reconstructed. The forthcoming improvements of all these techniques are discussed.Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Livet, F.2007-03-01doi:10.1107/S010876730605570XInternational Union of CrystallographyTechniques for coherent X-ray scattering measurements are detailed. Applications in the study of the dynamics of fluctuations and in lensless high-resolution imaging are described.enCOHERENT X-RAY BEAMS; DYNAMICS OF FLUCTUATIONS; LENSLESS IMAGING; SMALL-ANGLE SET-UPSMethods for carrying out coherent X-ray scattering experiments are reviewed. The brilliance of the available synchrotron sources, the characteristics of the existing optics, the various ways of obtaining a beam of controlled coherence properties and the detectors used are summarized. Applications in the study of the dynamics of speckle patterns are described. In the case of soft condensed matter, the movement of inclusions like fillers in polymers or colloidal particles can be observed and these can reflect polymer or liquid-crystal fluctuations. In hard condensed-matter problems, like phase transitions, charge-density waves or phasons in quasicrystals, the study of speckle fluctuations provides new time-resolved methods. In the domain of lensless imaging, the coherent beam gives the modulus of the sample Fourier transform. If oversampling conditions are fulfilled, the phase can be obtained and the image in the direct space can be reconstructed. The forthcoming improvements of all these techniques are discussed.text/htmlDiffraction with a coherent X-ray beam: dynamics and imagingtext2632007-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673lead articles87med@iucr.org1071600-5724Nominations for the Ewald Prize
http://scripts.iucr.org/cgi-bin/paper?es0359
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-76732007-01-01doi:10.1107/S0108767306053992International Union of Crystallographyentext/htmlNominations for the Ewald Prizetext1632007-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673international union of crystallography80med@iucr.org801600-5724Structure determination from powder diffraction data. International Union of Crystallography Monographs in Crystallography. No. 13. Edited by W. I. F. David, K. Shankland, L. B. McCusker and Ch. Baerlocher. Pp. xix + 337. Oxford University Press, 2006. Price (paperback) GBP 39.95. ISBN 978-0-19-920553-0.
http://scripts.iucr.org/cgi-bin/paper?pf0038
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Paufler, P.2007-05-01doi:10.1107/S0108767306047349International Union of CrystallographyenBOOK RECEIVEDtext/htmlStructure determination from powder diffraction data. International Union of Crystallography Monographs in Crystallography. No. 13. Edited by W. I. F. David, K. Shankland, L. B. McCusker and Ch. Baerlocher. Pp. xix + 337. Oxford University Press, 2006. Price (paperback) GBP 39.95. ISBN 978-0-19-920553-0.text3632007-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673books received288med@iucr.org2881600-5724Structure and chemistry of crystalline solids. By B. E. Douglas and S.-M. Ho. Pp. x + 346. New York: Springer Science and Business Media, 2006. Price (hardback) EUR 99.95, USD 129.00, GBP 77.00. ISBN 978-0-387-26147-8.
http://scripts.iucr.org/cgi-bin/paper?pf0041
Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Paufler, P.2007-05-01doi:10.1107/S010876730701149XInternational Union of CrystallographyenBOOK RECEIVEDtext/htmlStructure and chemistry of crystalline solids. By B. E. Douglas and S.-M. Ho. Pp. x + 346. New York: Springer Science and Business Media, 2006. Price (hardback) EUR 99.95, USD 129.00, GBP 77.00. ISBN 978-0-387-26147-8.text3632007-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673books received288med@iucr.org2881600-5724Multiple twinning in cubic crystals: geometric/algebraic study and its application for the identification of the Σ3n grain boundaries
http://scripts.iucr.org/cgi-bin/paper?au5046
Multiple twinning in cubic crystals is represented geometrically by a three-dimensional fractal and algebraically by a groupoid. In this groupoid, the variant crystals are the objects, the misorientations between the variants are the operations, and the Σ3n operators are the different types of operations (expressed by sets of equivalent operations). A general formula gives the number of variants and the number of Σ3n operators for any twinning order. Different substructures of this groupoid (free group, semigroup) can be equivalently introduced to encode the operations with strings. For any coding substructure, the operators are expressed by sets of equivalent strings. The composition of two operators is determined without any matrix calculation by string concatenations. It is multivalued due to the groupoid structure. The composition table of the operators is used to identify the Σ3n grain boundaries and to reconstruct the twin related domains in the electron back-scattered diffraction maps.Copyright (c) 2007 International Union of Crystallographyurn:issn:0108-7673Cayron, C.2007-01-01doi:10.1107/S0108767306044291International Union of CrystallographyMultiple twinning in cubic crystals is represented geometrically by three-dimensional fractals and algebraically by groupoids. The groupoid composition table can be used to identify the Σ3n grain boundaries in EBSD maps.enELECTRON BACK-SCATTER DIFFRACTION (EBSD); FRACTAL; GROUPOID; MULTIPLE TWINNING; TWIN RELATED DOMAIN (TRD)Multiple twinning in cubic crystals is represented geometrically by a three-dimensional fractal and algebraically by a groupoid. In this groupoid, the variant crystals are the objects, the misorientations between the variants are the operations, and the Σ3n operators are the different types of operations (expressed by sets of equivalent operations). A general formula gives the number of variants and the number of Σ3n operators for any twinning order. Different substructures of this groupoid (free group, semigroup) can be equivalently introduced to encode the operations with strings. For any coding substructure, the operators are expressed by sets of equivalent strings. The composition of two operators is determined without any matrix calculation by string concatenations. It is multivalued due to the groupoid structure. The composition table of the operators is used to identify the Σ3n grain boundaries and to reconstruct the twin related domains in the electron back-scattered diffraction maps.text/htmlMultiple twinning in cubic crystals: geometric/algebraic study and its application for the identification of the Σ3n grain boundariestext1632007-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2007 International Union of Crystallography0108-7673research papers11med@iucr.org291600-5724On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model
http://scripts.iucr.org/cgi-bin/paper?sh5048
Accurate, yet simple and efficient, formulae are presented for calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) from the aspherical Hansen–Coppens pseudoatom model of electron density [Hansen & Coppens (1978). Acta Cryst. A34, 909–921]. They are based on the expansion of |r′ − r|−1 in spherical harmonics and the incomplete gamma function for a Slater-type function of the form Rl(r) = rn exp(−αr). The formulae are valid for 0 ≤ r ≤ ∞ and are easily extended to higher values of l. Special treatment of integrals is needed only for functions with n = l and n = l + 1 at r = 0. The method is tested using theoretical pseudoatom parameters of the formamide molecule obtained via reciprocal-space fitting of PBE/6-31G** densities and experimental X-ray data of Fe(CO)5. The ESP, EF and EFG values at the nuclear positions in formamide are in very good agreement with those directly evaluated from density-functional PBE calculations with 6-31G**, aug-cc-pVDZ and aug-cc-pVTZ basis sets. The small observed discrepancies are attributed to the different behavior of Gaussian- and Slater-type functions near the nuclei and to imperfections of the reciprocal-space fit. An EF map is displayed which allows useful visualization of the lattice EF effects in the crystal structure of formamide. Analysis of experimental 100 K X-ray data of Fe(CO)5 yields the value of the nuclear quadrupole moment Q(57Fem) = 0.12 × 10−28 m2 after taking into account Sternheimer shielding/antishielding effects of the core. This value is in excellent agreement with that reported by Su & Coppens [Acta Cryst. (1996), A52, 748–756] but slightly smaller than the generally accepted value of 0.16 ± 5% × 10−28 m2 obtained from combined theoretical/spectroscopic studies [Dufek, Blaha & Schwarz (1995). Phys. Rev. Lett. 25, 3545–3548].Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Volkov, A.King, H.F.Coppens, P.Farrugia, L.J.2006-09-01doi:10.1107/S0108767306026298International Union of CrystallographyAccurate, simple and efficient formulae for calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model of electron density are presented. The expressions are applied to the determination of the nuclear quadrupole moment of the Fe atom in Fe(CO)5.enASPHERICAL PSEUDOATOM MODEL; ELECTRIC FIELD; ELECTRIC FIELD GRADIENT; ELECTROSTATIC POTENTIALAccurate, yet simple and efficient, formulae are presented for calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) from the aspherical Hansen–Coppens pseudoatom model of electron density [Hansen & Coppens (1978). Acta Cryst. A34, 909–921]. They are based on the expansion of |r′ − r|−1 in spherical harmonics and the incomplete gamma function for a Slater-type function of the form Rl(r) = rn exp(−αr). The formulae are valid for 0 ≤ r ≤ ∞ and are easily extended to higher values of l. Special treatment of integrals is needed only for functions with n = l and n = l + 1 at r = 0. The method is tested using theoretical pseudoatom parameters of the formamide molecule obtained via reciprocal-space fitting of PBE/6-31G** densities and experimental X-ray data of Fe(CO)5. The ESP, EF and EFG values at the nuclear positions in formamide are in very good agreement with those directly evaluated from density-functional PBE calculations with 6-31G**, aug-cc-pVDZ and aug-cc-pVTZ basis sets. The small observed discrepancies are attributed to the different behavior of Gaussian- and Slater-type functions near the nuclei and to imperfections of the reciprocal-space fit. An EF map is displayed which allows useful visualization of the lattice EF effects in the crystal structure of formamide. Analysis of experimental 100 K X-ray data of Fe(CO)5 yields the value of the nuclear quadrupole moment Q(57Fem) = 0.12 × 10−28 m2 after taking into account Sternheimer shielding/antishielding effects of the core. This value is in excellent agreement with that reported by Su & Coppens [Acta Cryst. (1996), A52, 748–756] but slightly smaller than the generally accepted value of 0.16 ± 5% × 10−28 m2 obtained from combined theoretical/spectroscopic studies [Dufek, Blaha & Schwarz (1995). Phys. Rev. Lett. 25, 3545–3548].text/htmlOn the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom modeltext5622006-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673research papers400med@iucr.org4081600-5724Cristallographie. Deuxième édition, revue et augmentée. By D. Schwarzenbach and G. Chapuis. Lausanne: Presses Polytechniques et Universitaires Romandes, 2006. Pp. x + 344. In French. Price (softcover) CHF 79.50 (Switzerland), EUR 55.45 (other countries). ISBN 2-88074-672-8.
http://scripts.iucr.org/cgi-bin/paper?pf0035
Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Authier, A.2006-11-01doi:10.1107/S010876730602616XInternational Union of CrystallographyenBOOK REVIEWtext/htmlCristallographie. Deuxième édition, revue et augmentée. By D. Schwarzenbach and G. Chapuis. Lausanne: Presses Polytechniques et Universitaires Romandes, 2006. Pp. x + 344. In French. Price (softcover) CHF 79.50 (Switzerland), EUR 55.45 (other countries). ISBN 2-88074-672-8.text6622006-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673book reviews464med@iucr.org4641600-5724International tables for crystallography, Vol. G: Definition and exchange of crystallographic data. Edited by Sydney Hall and Brian McMahon. Dordrecht: Springer, 2005. Pp. xii + 594. Price (hardback) EUR 205.00, USD 220.00, GBP 135.00 for institutions; EUR 102.50, USD 110.00, GBP 67.50 for individuals. ISBN 1-4020-3138-6.
http://scripts.iucr.org/cgi-bin/paper?pf0032
Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Goddard, R.2006-11-01doi:10.1107/S0108767306023348International Union of CrystallographyenBOOK REVIEWtext/htmlInternational tables for crystallography, Vol. G: Definition and exchange of crystallographic data. Edited by Sydney Hall and Brian McMahon. Dordrecht: Springer, 2005. Pp. xii + 594. Price (hardback) EUR 205.00, USD 220.00, GBP 135.00 for institutions; EUR 102.50, USD 110.00, GBP 67.50 for individuals. ISBN 1-4020-3138-6.text6622006-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673book reviews463med@iucr.org4641600-5724The formation of low-dimensional metal trihalide crystals in carbon nanotubes
http://scripts.iucr.org/cgi-bin/paper?lb5002
Molecular dynamics computer simulation models are employed to study the direct filling of single-walled carbon nanotubes (which vary in diameter) with an archetypal metal trihalide, LaCl3. The use of relatively simple potential models allows the investigation of details of both the atomistic filling mechanism and the thermodynamic factors controlling the formation. The resulting low-dimensional crystallites are analysed with respect to bulk crystal structures and compared to experimental high-resolution transmission-electron-microscopy images by simulation of equivalent micrographs from one of the obtained potential models, resulting in excellent agreement between the simulated and experimental images.Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Wilson, M.Friedrichs, S.2006-07-01doi:10.1107/S0108767306018101International Union of CrystallographyAn MX3 stoichiometry salt, LaCl3, is shown to fill carbon nanotubes, of varying diameter, via molecular dynamics computer simulations to produce low-dimension crystals. The filled crystal structures allow a full atomistic comparison to be made with experimental high-resolution transmission electron micrographs, and the emergence of new, non-bulk, crystal structures is predicted.enCARBON NANOTUBES; METAL TRIHALIDESMolecular dynamics computer simulation models are employed to study the direct filling of single-walled carbon nanotubes (which vary in diameter) with an archetypal metal trihalide, LaCl3. The use of relatively simple potential models allows the investigation of details of both the atomistic filling mechanism and the thermodynamic factors controlling the formation. The resulting low-dimensional crystallites are analysed with respect to bulk crystal structures and compared to experimental high-resolution transmission-electron-microscopy images by simulation of equivalent micrographs from one of the obtained potential models, resulting in excellent agreement between the simulated and experimental images.text/htmlThe formation of low-dimensional metal trihalide crystals in carbon nanotubestext4622006-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673research papers287med@iucr.org2951600-5724Cristallographie. Deuxième édition revue et augmentée. Par Dieter Schwarzenbach et Gervais Chapuis. Paris: Presses Polytechniques et Universitaires Romandes, 2006. Pp. xii + 344. Prix broché EUR 55.45. ISBN 2-88074-672-8.
http://scripts.iucr.org/cgi-bin/paper?pf0030
Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Paufler, P.P.2006-07-01doi:10.1107/S0108767306014826International Union of CrystallographyenBOOK RECEIVEDtext/htmlCristallographie. Deuxième édition revue et augmentée. Par Dieter Schwarzenbach et Gervais Chapuis. Paris: Presses Polytechniques et Universitaires Romandes, 2006. Pp. xii + 344. Prix broché EUR 55.45. ISBN 2-88074-672-8.text4622006-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673books received318med@iucr.org3181600-5724Franz Ernst Neumann (1798–1895). Zum 200. Geburtstag des Mathematikers, Physikers und Kristallographen. Herausgeber R. Fritsch, E. Neumann-Redlin-von Neumann und T. J. Schenck. (Bilingual German/Russian.) Kaliningrad und München: Terra Baltica und Ludwig-Maximilians-Universität, 2005. 252 Seiten. Broschiert Preis: EUR 10. ISBN 5-98777-005-X, 3-922480-17-9.
http://scripts.iucr.org/cgi-bin/paper?pf0029
Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Paufler, P.P.2006-07-01doi:10.1107/S0108767306014814International Union of CrystallographyenBOOK RECEIVEDtext/htmlFranz Ernst Neumann (1798–1895). Zum 200. Geburtstag des Mathematikers, Physikers und Kristallographen. Herausgeber R. Fritsch, E. Neumann-Redlin-von Neumann und T. J. Schenck. (Bilingual German/Russian.) Kaliningrad und München: Terra Baltica und Ludwig-Maximilians-Universität, 2005. 252 Seiten. Broschiert Preis: EUR 10. ISBN 5-98777-005-X, 3-922480-17-9.text4622006-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673books received318med@iucr.org3181600-5724International tables for crystallography, Vol. D: Physical properties of crystals. Edited by André Authier. Dordrecht/Boston/London: Kluwer Academic Publishers, 2003. Pp. 522 + xii + CD-ROM. Price GBP 135, EUR 205, USD 220. ISBN 1-4020-0714-0.
http://scripts.iucr.org/cgi-bin/paper?pf0001
Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673 Paufler, P.2006-07-01doi:10.1107/S0108767306012001International Union of CrystallographyenBOOK REVIEWtext/htmlInternational tables for crystallography, Vol. D: Physical properties of crystals. Edited by André Authier. Dordrecht/Boston/London: Kluwer Academic Publishers, 2003. Pp. 522 + xii + CD-ROM. Price GBP 135, EUR 205, USD 220. ISBN 1-4020-0714-0.text4622006-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673book reviews316med@iucr.org3181600-5724Robert Crispin Evans (1909–2005)
http://scripts.iucr.org/cgi-bin/paper?es0350
Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Cruickshank, D.2006-05-01doi:10.1107/S0108767306005563International Union of CrystallographyenOBITUARYtext/htmlRobert Crispin Evans (1909–2005)text3622006-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673obituaries147med@iucr.org1511600-5724International School on Mathematical and Theoretical Crystallography
http://scripts.iucr.org/cgi-bin/paper?me0314
Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Nespolo, M.2006-03-01doi:10.1107/S0108767306004521International Union of CrystallographyenPREFACE; MATHCRYSTtext/htmlInternational School on Mathematical and Theoretical Crystallographytext2622006-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673issue prefacemed@iucr.org1600-5724Application of modern tensor calculus to engineered domain structures. 2. Tensor distinction of domain states
http://scripts.iucr.org/cgi-bin/paper?xo5008
The theory of domain states is reviewed as a prerequisite for consideration of tensorial distinction of domain states. It is then shown that the parameters of the first domain in a ferroic phase transition from a set of isomorphic groups of the same oriented Laue class can be systematically and suitably represented in terms of typical variables. On replacing these variables by actual tensor components according to the previous paper [Kopský (2006), Acta Cryst. A62, 47–64], we can reveal the tensorial parameters associated with each particular symmetry descent. Parameters are distinguished by the ireps to which they belong and this can be used to determine which of them are the principal parameters that distinguish all domain states, in contrast to secondary parameters which are common to several domain states. In general, the parameters are expressed as the covariant components of the tensors. A general procedure is described which is designed to transform the results to Cartesian components. It consists of two parts: the first, called the labelling of covariants, and its inverse, called the conversion equations. Transformation of parameters from the first domain state to other states is now reduced to irreducible subspaces whose maximal dimension is three in contrast with higher dimensions of tensor spaces. With this method, we can explicitly calculate tensor parameters for all domain states. To find the distinction of pairs of domain states, it is suitable to use the concept of the twinning group which is briefly described.Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Kopský, V.2006-03-01doi:10.1107/S010876730600078XInternational Union of CrystallographyTensor parameters of domain states in ferroic phase transitions are considered. It is shown how to find both primary and secondary parameters from the decomposition of tensors into covariants.enDOMAIN STRUCTURES; TENSOR CALCULUSThe theory of domain states is reviewed as a prerequisite for consideration of tensorial distinction of domain states. It is then shown that the parameters of the first domain in a ferroic phase transition from a set of isomorphic groups of the same oriented Laue class can be systematically and suitably represented in terms of typical variables. On replacing these variables by actual tensor components according to the previous paper [Kopský (2006), Acta Cryst. A62, 47–64], we can reveal the tensorial parameters associated with each particular symmetry descent. Parameters are distinguished by the ireps to which they belong and this can be used to determine which of them are the principal parameters that distinguish all domain states, in contrast to secondary parameters which are common to several domain states. In general, the parameters are expressed as the covariant components of the tensors. A general procedure is described which is designed to transform the results to Cartesian components. It consists of two parts: the first, called the labelling of covariants, and its inverse, called the conversion equations. Transformation of parameters from the first domain state to other states is now reduced to irreducible subspaces whose maximal dimension is three in contrast with higher dimensions of tensor spaces. With this method, we can explicitly calculate tensor parameters for all domain states. To find the distinction of pairs of domain states, it is suitable to use the concept of the twinning group which is briefly described.text/htmlApplication of modern tensor calculus to engineered domain structures. 2. Tensor distinction of domain statestext2622006-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673feature articles65med@iucr.org761600-5724Application of modern tensor calculus to engineered domain structures. 1. Calculation of tensorial covariants
http://scripts.iucr.org/cgi-bin/paper?xo5007
This article is a roadmap to a systematic calculation and tabulation of tensorial covariants for the point groups of material physics. The following are the essential steps in the described approach to tensor calculus. (i) An exact specification of the considered point groups by their embellished Hermann–Mauguin and Schoenflies symbols. (ii) Introduction of oriented Laue classes of magnetic point groups. (iii) An exact specification of matrix ireps (irreducible representations). (iv) Introduction of so-called typical (standard) bases and variables – typical invariants, relative invariants or components of the typical covariants. (v) Introduction of Clebsch–Gordan products of the typical variables. (vi) Calculation of tensorial covariants of ascending ranks with consecutive use of tables of Clebsch–Gordan products. (vii) Opechowski's magic relations between tensorial decompositions. These steps are illustrated for groups of the tetragonal oriented Laue class D4z − 4z2x2xy of magnetic point groups and for tensors up to fourth rank.Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Kopský, V.2006-03-01doi:10.1107/S0108767306000778International Union of CrystallographyA systematic approach to calculation of the decomposition of material tensors, including magnetic properties, into tensorial covariants is described.enDOMAIN STRUCTURES; TENSOR CALCULUSThis article is a roadmap to a systematic calculation and tabulation of tensorial covariants for the point groups of material physics. The following are the essential steps in the described approach to tensor calculus. (i) An exact specification of the considered point groups by their embellished Hermann–Mauguin and Schoenflies symbols. (ii) Introduction of oriented Laue classes of magnetic point groups. (iii) An exact specification of matrix ireps (irreducible representations). (iv) Introduction of so-called typical (standard) bases and variables – typical invariants, relative invariants or components of the typical covariants. (v) Introduction of Clebsch–Gordan products of the typical variables. (vi) Calculation of tensorial covariants of ascending ranks with consecutive use of tables of Clebsch–Gordan products. (vii) Opechowski's magic relations between tensorial decompositions. These steps are illustrated for groups of the tetragonal oriented Laue class D4z − 4z2x2xy of magnetic point groups and for tensors up to fourth rank.text/htmlApplication of modern tensor calculus to engineered domain structures. 1. Calculation of tensorial covariantstext2622006-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673feature articles47med@iucr.org641600-5724Groupoid of orientational variants
http://scripts.iucr.org/cgi-bin/paper?pz5027
Daughter crystals in orientation relationship with a parent crystal are called variants. They can be created by a structural phase transition (Landau or reconstructive), by twinning or by precipitation. Internal and external classes of transformations defined from the point groups of the parent and daughter phases and from a transformation matrix allow the orientations of the distinct variants to be determined. These are algebraically identified with left cosets and their number is given by the Lagrange formula. A simple equation links the numbers of variants of the direct and inverse transitions. The equivalence classes on the transformations between variants are isomorphic to the double cosets (operators) and their number is given by the Burnside formula. The orientational variants and the operators constitute a groupoid whose composition table acts as a crystallographic signature of the transition. A general method that determines if two daughter variants can be inherited from more than one parent crystal is also described. A computer program has been written to calculate all these properties for any structural transition; some results are given for Burgers transitions and for martensitic transitions in steels. The complexity, irreversibility and entropy of fractal systems constituted by orientational variants generated by thermal cycling are briefly discussed.Copyright (c) 2006 International Union of Crystallographyurn:issn:0108-7673Cayron, C.2006-01-01doi:10.1107/S010876730503686XInternational Union of CrystallographyThe orientational variants generated by twinning, precipitation or phase transition are algebraically described by a groupoid theory.enCOSET; GROUPOID; ORIENTATION; PHASE TRANSITION; SYMMETRY; VARIANTDaughter crystals in orientation relationship with a parent crystal are called variants. They can be created by a structural phase transition (Landau or reconstructive), by twinning or by precipitation. Internal and external classes of transformations defined from the point groups of the parent and daughter phases and from a transformation matrix allow the orientations of the distinct variants to be determined. These are algebraically identified with left cosets and their number is given by the Lagrange formula. A simple equation links the numbers of variants of the direct and inverse transitions. The equivalence classes on the transformations between variants are isomorphic to the double cosets (operators) and their number is given by the Burnside formula. The orientational variants and the operators constitute a groupoid whose composition table acts as a crystallographic signature of the transition. A general method that determines if two daughter variants can be inherited from more than one parent crystal is also described. A computer program has been written to calculate all these properties for any structural transition; some results are given for Burgers transitions and for martensitic transitions in steels. The complexity, irreversibility and entropy of fractal systems constituted by orientational variants generated by thermal cycling are briefly discussed.text/htmlGroupoid of orientational variantstext1622006-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2006 International Union of Crystallography0108-7673research papers21med@iucr.org401600-5724Ab initio structure determination using dispersive differences from multiple-wavelength synchrotron-radiation powder diffraction data
http://scripts.iucr.org/cgi-bin/paper?sh5034
The purpose of this paper and a test case study is to assess a method of ab initio structure solution from powder diffraction data using f′ difference techniques. A theoretical foundation for the approach used is first provided. Then, with a test case (nickel sulfate hexahydrate), it is shown that both the position of the anomalous scatterer (Ni) can be determined and the structure can be developed in full. Specifically, synchrotron-radiation data were collected at two wavelengths close to the K edge for Ni and three wavelengths remote from the Ni absorption edge, at 1.3, 1.8 and 2.16 Å. These five wavelengths then allowed various combinations to be tried to establish which wavelength pairs gave the optimum signal in the Patterson maps using dispersive amplitude differences. The initial phases derived from the metal-atom position then allowed the structure to be fully developed by difference Fourier cycling. The relevance of these developments to structure-solution possibilities for proteins via powder dispersive difference data is then outlined.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Helliwell, J.R.Helliwell, M.Jones, R.H.2005-11-01doi:10.1107/S010876730503237XInternational Union of CrystallographyA theoretical foundation and test-case evaluation is presented for de novo structure determination using f′ difference techniques. Prospects for extension of these methods to larger molecules than are currently tackled, including proteins, and the possible use of softer X-rays are discussed.enANOMALOUS SCATTERING; POWDER DIFFRACTION; PROTEIN MICROCRYSTALS; SYNCHROTRON RADIATIONThe purpose of this paper and a test case study is to assess a method of ab initio structure solution from powder diffraction data using f′ difference techniques. A theoretical foundation for the approach used is first provided. Then, with a test case (nickel sulfate hexahydrate), it is shown that both the position of the anomalous scatterer (Ni) can be determined and the structure can be developed in full. Specifically, synchrotron-radiation data were collected at two wavelengths close to the K edge for Ni and three wavelengths remote from the Ni absorption edge, at 1.3, 1.8 and 2.16 Å. These five wavelengths then allowed various combinations to be tried to establish which wavelength pairs gave the optimum signal in the Patterson maps using dispersive amplitude differences. The initial phases derived from the metal-atom position then allowed the structure to be fully developed by difference Fourier cycling. The relevance of these developments to structure-solution possibilities for proteins via powder dispersive difference data is then outlined.text/htmlAb initio structure determination using dispersive differences from multiple-wavelength synchrotron-radiation powder diffraction datatext6612005-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673research papers568med@iucr.org5741600-5724Report of the Working Group on Crystal Phase Identifiers
http://scripts.iucr.org/cgi-bin/paper?me0302
The proposed crystalline phase identifier consists of a number of components (layers) describing enough properties of the phase to allow a unique identification. These layers consist of the chemical formula, a flag indicating the state of matter, the space-group number and the Wyckoff sequence. They are defined in such a way that they can be incorporated into the IUPAC International Chemical Identifier (InChI) proposed by the International Union of Pure and Applied Chemistry (IUPAC).Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Brown, I.D.Abrahams, S.C.Berndt, M.Faber, J.Karen, V.L.Motherwell, W.D.S.Villars, P.Westbrook, J.D.McMahon, B.2005-11-01doi:10.1107/S010876730503179XInternational Union of CrystallographyThe proposed crystalline phase identifier consists of a number of components (layers) describing enough properties of the phase to allow a unique identification. These layers consist of the chemical formula, a flag indicating the state of matter, the space-group number and the Wyckoff sequence. They are defined in such a way that they can be incorporated into the IUPAC International Chemical Identifier (InChI) proposed by the International Union of Pure and Applied Chemistry (IUPAC).enCRYSTAL PHASE IDENTIFIERS; NOMENCLATUREThe proposed crystalline phase identifier consists of a number of components (layers) describing enough properties of the phase to allow a unique identification. These layers consist of the chemical formula, a flag indicating the state of matter, the space-group number and the Wyckoff sequence. They are defined in such a way that they can be incorporated into the IUPAC International Chemical Identifier (InChI) proposed by the International Union of Pure and Applied Chemistry (IUPAC).text/htmlReport of the Working Group on Crystal Phase Identifierstext6612005-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673research papers575med@iucr.org5801600-5724Electron crystallography of zeolites – the MWW family as a test of direct 3D structure determination
http://scripts.iucr.org/cgi-bin/paper?gc0052
The efficacy of direct methods for solving the crystal structures of zeolites from electron diffraction data is evaluated for a series of related materials, i.e. MCM-22, MCM-49 and ITQ-1. First, it is established by tilting experiments that all materials share the same MWW framework. The calcined product of a delaminated MCM-22 precursor, ITQ-2, also shares this framework structure within the limited number of stacked unit cells. For all materials, the underlying space group is P6/mmm where a ≃ 14.21, c ≃ 24.94 Å. Traditional direct methods are useful for determining the projected structure down the hexagonal axis but are not very effective for finding the three-dimensional structure. On the other hand, maximum-entropy and likelihood approaches are effective for determining either 2D projections or 3D frameworks. The major restriction to 3D determinations by direct methods is the limited goniometric tilt range of the electron microscope, hence the `missing cone' of information. Potential maps from the most accurate phase sets are, therefore, observed as continuous density envelopes to the true structure. Some improvement is found when the Sayre equation predicts missing amplitudes and phases but it is clear that better specimen preparation methods are required to include projections containing the c∗ axis of the reciprocal lattice.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Dorset, D.L.Roth, W.J.Gilmore, C.J.2005-09-01doi:10.1107/S0108767305024670International Union of CrystallographyThe 3D crystal structure of zeolites in the MWW framework family is determined from electron diffraction intensities by direct phasing using maximum entropy and likelihood. Although the `missing cone' left from incomplete goniometric data sampling leads to a somewhat distorted model, the true zeolite framework geometry may be recovered by imposing conservative bonding restraints.enELECTRON CRYSTALLOGRAPHY; ZEOLITESThe efficacy of direct methods for solving the crystal structures of zeolites from electron diffraction data is evaluated for a series of related materials, i.e. MCM-22, MCM-49 and ITQ-1. First, it is established by tilting experiments that all materials share the same MWW framework. The calcined product of a delaminated MCM-22 precursor, ITQ-2, also shares this framework structure within the limited number of stacked unit cells. For all materials, the underlying space group is P6/mmm where a ≃ 14.21, c ≃ 24.94 Å. Traditional direct methods are useful for determining the projected structure down the hexagonal axis but are not very effective for finding the three-dimensional structure. On the other hand, maximum-entropy and likelihood approaches are effective for determining either 2D projections or 3D frameworks. The major restriction to 3D determinations by direct methods is the limited goniometric tilt range of the electron microscope, hence the `missing cone' of information. Potential maps from the most accurate phase sets are, therefore, observed as continuous density envelopes to the true structure. Some improvement is found when the Sayre equation predicts missing amplitudes and phases but it is clear that better specimen preparation methods are required to include projections containing the c∗ axis of the reciprocal lattice.text/htmlElectron crystallography of zeolites – the MWW family as a test of direct 3D structure determinationtext5612005-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673research papers516med@iucr.org5271600-5724Polarization anisotropy of X-ray atomic factors and `forbidden' resonant reflections
http://scripts.iucr.org/cgi-bin/paper?sh0182
Symmetry and physical aspects of `forbidden' reflections excited by a local polarization anisotropy of the X-ray susceptibility are surveyed. Such reflections are observed near absorption edges where the anisotropy is caused by distortions of the atomic electronic states owing to interaction with neighbouring atoms. As a consequence, they allow for extracting nontrivial information about the resonant atom's local environment and their physical conditions. The unusual polarization properties of the considered reflections are helpful to distinguish them from other types of `forbidden' reflections. When such reflections are excited, it is, for example, possible to determine not only the intrinsic anisotropy of an atomic form factor but also additional anisotropy induced by thermal motion, point defects and/or incommensurate modulations. Even the local `chirality' of atoms in centrosymmetric crystals is accessible. Unsolved key problems and possible future developments are addressed.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Dmitrienko, V.E.Ishida, K.Kirfel, A.Ovchinnikova, E.N.2005-09-01doi:10.1107/S0108767305018209International Union of CrystallographyIn the resonant region near an absorption edge, a polarization anisotropy of the local X-ray susceptibility results in additional reflections otherwise forbidden by screw-axis and/or glide-plane extinction rules.enFORBIDDEN REFLECTIONS; RESONANT X-RAY DIFFRACTION; X-RAY ANISOTROPYSymmetry and physical aspects of `forbidden' reflections excited by a local polarization anisotropy of the X-ray susceptibility are surveyed. Such reflections are observed near absorption edges where the anisotropy is caused by distortions of the atomic electronic states owing to interaction with neighbouring atoms. As a consequence, they allow for extracting nontrivial information about the resonant atom's local environment and their physical conditions. The unusual polarization properties of the considered reflections are helpful to distinguish them from other types of `forbidden' reflections. When such reflections are excited, it is, for example, possible to determine not only the intrinsic anisotropy of an atomic form factor but also additional anisotropy induced by thermal motion, point defects and/or incommensurate modulations. Even the local `chirality' of atoms in centrosymmetric crystals is accessible. Unsolved key problems and possible future developments are addressed.text/htmlPolarization anisotropy of X-ray atomic factors and `forbidden' resonant reflectionstext5612005-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673topical reviews481med@iucr.org4931600-5724Rapid calculation of RMSDs using a quaternion-based characteristic polynomial
http://scripts.iucr.org/cgi-bin/paper?sh5029
A common measure of conformational similarity in structural bioinformatics is the minimum root mean square deviation (RMSD) between the coordinates of two macromolecules. In many applications, the rotations relating the structures are not needed. Several common algorithms for calculating RMSDs require the computationally costly procedures of determining either the eigen decomposition or matrix inversion of a 3\times3 or 4\times4 matrix. Using a quaternion-based method, here a simple algorithm is developed that rapidly and stably determines RMSDs by circumventing the decomposition and inversion problems.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Theobald, D.L.2005-07-01doi:10.1107/S0108767305015266International Union of CrystallographyUsing a quaternion-based characteristic polynomial, a simple algorithm is developed that rapidly and stably determines root mean square deviations for structural superpositions.enCHARACTERISTIC EQUATION; QUARTIC POLYNOMIAL; QUATERNION; RMSD; SUPERPOSITIONA common measure of conformational similarity in structural bioinformatics is the minimum root mean square deviation (RMSD) between the coordinates of two macromolecules. In many applications, the rotations relating the structures are not needed. Several common algorithms for calculating RMSDs require the computationally costly procedures of determining either the eigen decomposition or matrix inversion of a 3\times3 or 4\times4 matrix. Using a quaternion-based method, here a simple algorithm is developed that rapidly and stably determines RMSDs by circumventing the decomposition and inversion problems.text/htmlRapid calculation of RMSDs using a quaternion-based characteristic polynomialtext4612005-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673short communications478med@iucr.org4801600-5724Crystallography of modular materials. By Giovanni Ferraris, Emil Makovicky and Stefano Merlino. Pp. x + 370. Oxford: Oxford University Press, 2004. Price Hardback GBP 75.00. ISBN 0-19-852664-4.
http://scripts.iucr.org/cgi-bin/paper?pf0014
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Durovič, S.2005-09-01doi:10.1107/S0108767305004307International Union of CrystallographyenBOOK REVIEWtext/htmlCrystallography of modular materials. By Giovanni Ferraris, Emil Makovicky and Stefano Merlino. Pp. x + 370. Oxford: Oxford University Press, 2004. Price Hardback GBP 75.00. ISBN 0-19-852664-4.text5612005-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673book reviews531med@iucr.org5321600-5724Mario Nardelli (1922–2004)
http://scripts.iucr.org/cgi-bin/paper?es0342
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-76732005-03-01doi:10.1107/S0108767305002345International Union of Crystallographyentext/htmlMario Nardelli (1922–2004)text2612005-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673obituaries159med@iucr.org1611600-5724Crystal structure determination. Second edition. By Werner Massa. Pp. xi + 210. Translated into English by Robert O. Gould. Berlin: Springer, 2004. Price EUR 44.95, USD 49.95. ISBN 3-540-20644-2.
http://scripts.iucr.org/cgi-bin/paper?pf0009
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Glusker, J.P.2005-03-01doi:10.1107/S0108767305001285International Union of CrystallographyenBOOK REVIEWtext/htmlCrystal structure determination. Second edition. By Werner Massa. Pp. xi + 210. Translated into English by Robert O. Gould. Berlin: Springer, 2004. Price EUR 44.95, USD 49.95. ISBN 3-540-20644-2.text2612005-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673book reviews261med@iucr.org2621600-5724Light is a messenger – the life and science of William Lawrence Bragg. By G. K. Hunter. Pp. xxi + 301. Oxford: Oxford University Press, 2004. Price Hardback GBP 35.00. ISBN 0-19-852921-X.
http://scripts.iucr.org/cgi-bin/paper?pf0015
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673North, A.C.T.2005-03-01doi:10.1107/S0108767305001273International Union of CrystallographyenBOOK REVIEWtext/htmlLight is a messenger – the life and science of William Lawrence Bragg. By G. K. Hunter. Pp. xxi + 301. Oxford: Oxford University Press, 2004. Price Hardback GBP 35.00. ISBN 0-19-852921-X.text2612005-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673book reviews262med@iucr.org2641600-5724Themed issues of Acta Crystallographica Section A on phase transitions
http://scripts.iucr.org/cgi-bin/paper?me0287
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Pandey, D.2005-01-01doi:10.1107/S0108767304033434International Union of CrystallographyenPHASE TRANSITIONStext/htmlThemed issues of Acta Crystallographica Section A on phase transitionstext1612005-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673topical reviews1med@iucr.org21600-5724John M. Cowley FAA FRS (1923–2004)
http://scripts.iucr.org/cgi-bin/paper?es0338
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Moodie, A.2005-01-01doi:10.1107/S0108767304029484International Union of CrystallographyenOBITUARYtext/htmlJohn M. Cowley FAA FRS (1923–2004)text1612005-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673obituaries122med@iucr.org1241600-5724Mathematical techniques in crystallography and materials science. Third edition. By Edward Prince. Pp. vii + 224. Berlin and Heidelberg: Springer-Verlag, 2004. Price EUR 39.95 (soft cover). ISBN 3-540-21111-X.
http://scripts.iucr.org/cgi-bin/paper?pf0008
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Aroyo, M.2005-03-01doi:10.1107/S0108767304029186International Union of CrystallographyenBOOK REVIEWtext/htmlMathematical techniques in crystallography and materials science. Third edition. By Edward Prince. Pp. vii + 224. Berlin and Heidelberg: Springer-Verlag, 2004. Price EUR 39.95 (soft cover). ISBN 3-540-21111-X.text2612005-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673book reviews260med@iucr.org2611600-5724X-ray Compton scattering. By Malcolm J. Cooper, Peter E. Mijnarends, Nobuhiro Shiotani, Nobuhiko Sakai and Arun Bansil. Oxford: Oxford University Press, 2004, pp. XVII + 374. Price GPB 95.10. ISBN 0 19 850168 4.
http://scripts.iucr.org/cgi-bin/paper?pf5001
Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Paufler, P.P.2005-03-01doi:10.1107/S0108767304028569International Union of CrystallographyenBOOK RECEIVEDtext/htmlX-ray Compton scattering. By Malcolm J. Cooper, Peter E. Mijnarends, Nobuhiro Shiotani, Nobuhiko Sakai and Arun Bansil. Oxford: Oxford University Press, 2004, pp. XVII + 374. Price GPB 95.10. ISBN 0 19 850168 4.text2612005-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673books received264med@iucr.org2641600-5724Determination of depth-dependent diffraction data: a new approach
http://scripts.iucr.org/cgi-bin/paper?mm5009
A direct method for determining powder diffraction data at specific depths from angle-dependent diffraction data is described. The method is non-destructive and only traditional data collections, where the angle of incidence is varied, are required. These angle-dependent spectra are transformed to give diffraction data arising from different depths, which may then be exploited using any conventional method. This is a novel approach as traditional methods are forced to tolerate the inherent depth averaging of grazing-angle diffraction, or only examine specific structural characteristics. In order to obtain depth-dependent X-ray diffraction data, a Fredholm integral equation of the first kind is solved using regularization techniques. The method has been validated by the generation of pseudo-experimental data having known depth profiles and solving the Fredholm integral equation to recover the solution. The method has also been applied to experimental data from a number of thin film systems.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Broadhurst, A.Rogers, K.D.Lowe, T.W.Lane, D.W.2005-01-01doi:10.1107/S0108767304026881International Union of CrystallographyA direct method for transforming angle-dependent diffraction data into depth-dependent data by the use of regularization techniques is presented, including method validation and application to experimental data.enDEPTH PROFILING; FREDHOLM INTEGRAL EQUATION; REGULARIZATIONA direct method for determining powder diffraction data at specific depths from angle-dependent diffraction data is described. The method is non-destructive and only traditional data collections, where the angle of incidence is varied, are required. These angle-dependent spectra are transformed to give diffraction data arising from different depths, which may then be exploited using any conventional method. This is a novel approach as traditional methods are forced to tolerate the inherent depth averaging of grazing-angle diffraction, or only examine specific structural characteristics. In order to obtain depth-dependent X-ray diffraction data, a Fredholm integral equation of the first kind is solved using regularization techniques. The method has been validated by the generation of pseudo-experimental data having known depth profiles and solving the Fredholm integral equation to recover the solution. The method has also been applied to experimental data from a number of thin film systems.text/htmlDetermination of depth-dependent diffraction data: a new approachtext1612005-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673research papers139med@iucr.org1461600-5724X-ray studies of the phases and phase transitions of liquid crystals
http://scripts.iucr.org/cgi-bin/paper?pd5027
A short review is given of recent X-ray diffraction studies of the phases and phase transitions of thermotropic liquid crystals. The areas covered are twist-grain-boundary phases, antiferroelectric phases studied with resonant X-ray diffraction and smectic phases within gel structures. In all areas, X-ray diffraction has played a key role. Nonetheless, open questions remain: the nature of the smectic C variant of the twist-grain-boundary phase, the origin of antiferroelectric phases, and whether novel Bragg glass states exist for smectic A gel samples.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Clegg, P.S.2005-01-01doi:10.1107/S0108767304025991International Union of CrystallographyRecent X-ray diffraction studies of liquid crystals are reviewed. The topics are twist grain-boundary phases, antiferroelectric phases studied using resonant diffraction and smectic phases within gel structures.enLIQUID CRYSTALS; PHASE TRANSITIONSA short review is given of recent X-ray diffraction studies of the phases and phase transitions of thermotropic liquid crystals. The areas covered are twist-grain-boundary phases, antiferroelectric phases studied with resonant X-ray diffraction and smectic phases within gel structures. In all areas, X-ray diffraction has played a key role. Nonetheless, open questions remain: the nature of the smectic C variant of the twist-grain-boundary phase, the origin of antiferroelectric phases, and whether novel Bragg glass states exist for smectic A gel samples.text/htmlX-ray studies of the phases and phase transitions of liquid crystalstext1612005-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673topical reviews112med@iucr.org1211600-5724Mathematical techniques in crystallography and materials science. By Edward Prince. 3rd ed. Pp. XI + 224. Berlin, Heidelberg, New York: Springer-Verlag, 2004. Price (softcover) EUR 42.75. ISBN 3 540 21111 X.
http://scripts.iucr.org/cgi-bin/paper?pf0007
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Paufler, P.P.2004-11-01doi:10.1107/S0108767304021713International Union of Crystallographyentext/htmlMathematical techniques in crystallography and materials science. By Edward Prince. 3rd ed. Pp. XI + 224. Berlin, Heidelberg, New York: Springer-Verlag, 2004. Price (softcover) EUR 42.75. ISBN 3 540 21111 X.text6602004-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673books received642med@iucr.org6421600-5724Crystal structure determination. By Werner Massa. Second completely updated edition. Pp. XI + 210. Berlin, Heidelberg, New York: Springer-Verlag, 2004. Price EUR 48.10. ISBN 3 540 20644 2.
http://scripts.iucr.org/cgi-bin/paper?pf0003
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Paufler, P.P.2004-11-01doi:10.1107/S0108767304021701International Union of Crystallographyentext/htmlCrystal structure determination. By Werner Massa. Second completely updated edition. Pp. XI + 210. Berlin, Heidelberg, New York: Springer-Verlag, 2004. Price EUR 48.10. ISBN 3 540 20644 2.text6602004-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673books received642med@iucr.org6421600-5724Orientations and rotations. Computations in crystallographic textures. By Adam Morawiec. Pp. X + 200. Berlin, Heidelberg, New York: Springer-Verlag, 2004. Price EUR 59.95, GBP 46.00, USD 79.95. ISBN 3 540 40734 0.
http://scripts.iucr.org/cgi-bin/paper?pf0002
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Paufler, P.P.2004-11-01doi:10.1107/S0108767304021695International Union of Crystallographyentext/htmlOrientations and rotations. Computations in crystallographic textures. By Adam Morawiec. Pp. X + 200. Berlin, Heidelberg, New York: Springer-Verlag, 2004. Price EUR 59.95, GBP 46.00, USD 79.95. ISBN 3 540 40734 0.text6602004-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673books received642med@iucr.org6421600-5724The Peierls transition in low-dimensional electronic crystals
http://scripts.iucr.org/cgi-bin/paper?pd5028
An overview is presented of low-dimensional electronic crystals that undergo a phase transition towards a low-temperature charge-density-wave (CDW) state. The emphasis is on inorganic compounds that develop an one-dimensional (1D) CDW. Low-dimensional features of crystal structures are discussed in relation to 1D electronic properties. X-ray diffraction is discussed as a tool to obtain quantitative information about the normal state and its structural fluctuations, and about the CDW, both in equilibrium and in its non-linear conducting state.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Smaalen, S. van2005-01-01doi:10.1107/S0108767304025437International Union of CrystallographyAn overview is presented of inorganic compounds with low-dimensional electronic structures, and of X-ray diffraction as a tool to study the properties of charge-density waves (CDWs).enELECTRONIC CRYSTALS; PEIERLS TRANSITION; PHASE TRANSITIONSAn overview is presented of low-dimensional electronic crystals that undergo a phase transition towards a low-temperature charge-density-wave (CDW) state. The emphasis is on inorganic compounds that develop an one-dimensional (1D) CDW. Low-dimensional features of crystal structures are discussed in relation to 1D electronic properties. X-ray diffraction is discussed as a tool to obtain quantitative information about the normal state and its structural fluctuations, and about the CDW, both in equilibrium and in its non-linear conducting state.text/htmlThe Peierls transition in low-dimensional electronic crystalstext1612005-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673topical reviews51med@iucr.org611600-5724A strict solution for the optimal superimposition of protein structures. Retraction
http://scripts.iucr.org/cgi-bin/paper?sh0180
In the paper `A strict solution for the optimal superimposition of protein structures' by Chuanbo Chen & Qishen Li [Acta Cryst. (2004), A60, 201–203], we claimed that existing methods for the optimal superimposition of two point sets, requiring the precondition of coincident centroids, are mathematically not strict. It has been brought to our attention that this claim is erroneous. We therefore retract the publication.Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Chen, C.Li, Q.2004-11-01doi:10.1107/S0108767304024730International Union of CrystallographyThe manuscript that appeared in Acta Cryst. (2004), A60, 201–203 is retracted.enBIOINFORMATICS; PROTEIN STRUCTURE; OPTIMAL SUPERIMPOSITIONIn the paper `A strict solution for the optimal superimposition of protein structures' by Chuanbo Chen & Qishen Li [Acta Cryst. (2004), A60, 201–203], we claimed that existing methods for the optimal superimposition of two point sets, requiring the precondition of coincident centroids, are mathematically not strict. It has been brought to our attention that this claim is erroneous. We therefore retract the publication.text/htmlA strict solution for the optimal superimposition of protein structures. Retractiontext6602004-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673addenda and errata640med@iucr.org6401600-5724International tables for crystallography. Vol. A. 5th edition. Edited by Th. Hahn. Pp. xx + 911. Dordrecht: Kluwer Academic Publishers, 2002. Price EUR 242, GBP 142, USD 225. ISBN 0-7923-6590-9.
http://scripts.iucr.org/cgi-bin/paper?pf0012
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Paufler, P.2004-11-01doi:10.1107/S0108767304022536International Union of CrystallographyenBOOK REVIEWStext/htmlInternational tables for crystallography. Vol. A. 5th edition. Edited by Th. Hahn. Pp. xx + 911. Dordrecht: Kluwer Academic Publishers, 2002. Price EUR 242, GBP 142, USD 225. ISBN 0-7923-6590-9.text6602004-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673book reviews641med@iucr.org6421600-5724Ferroelastic phase transitions: structure and microstructure
http://scripts.iucr.org/cgi-bin/paper?pd5021
Landau-type theories describe the observed behaviour of phase transitions in ferroelastic and co-elastic minerals and materials with a high degree of accuracy. In this review, the derivation of the Landau potential G = ½AθS [coth(θS/T) − coth(θS/TC)]Q2 + ¼BQ4 + … is derived as a solution of the general φ4 model. The coupling between the order parameter and spontaneous strain of a phase transition brings the behaviour of many phase transitions to the mean-field limit, even when the atomistic mechanism of the transition is spin-like. Strain coupling is also a common mechanism for the coupling between multiple order parameters in a single system. As well as changes on the crystal structure scale, phase transitions modify the microstructure of materials, leading to anomalous mesoscopic features at domain boundaries. The mesostructure of a domain wall is studied experimentally using X-ray diffraction, and interpreted theoretically using Ginzburg–Landau theory. One important consequence of twin mesostructures is their modified transport properties relative to the bulk. Domain wall motion also provides a mechanism for superelastic behaviour in ferroelastics. At surfaces, the relaxations that occur can be described in terms of order parameters and Landau theory. This leads to an exponential profile of surface relaxations. This in turn leads to an exponential interaction energy between surfaces, which can, if large enough, destabilize symmetrical morphologies in favour of a platelet morphology. Surface relaxations may also affect the behaviour of twin walls as they intersect surfaces, since the surface relaxation may lead to an incompatibility of the two domains at the surface, generating large strains at the relaxation. Landau theory may also be extended to describe the kinetics of phase transitions. Time-dependent Landau theory may be used to describe the kinetics of order–disorder phase transitions in which the order parameter is homogeneous. However, the time-dependent Landau theory equations also have microstructural solutions, explaining the formation of microstructures such as tweed.Copyright (c) 2005 International Union of Crystallographyurn:issn:0108-7673Salje, E.K.H.Hayward, S.A.Lee, W.T.2005-01-01doi:10.1107/S0108767304020318International Union of CrystallographyThe uses of Landau-type theories to describe structural, microstructural and mesostructural features of materials undergoing phase transitions are reviewed.enANORTHITE; KINETICS; LANDAU THEORY; MESOSTRUCTURE; OMPHACITE; PHASE TRANSITIONS; STRAIN COUPLING; SUPERELASTICITY; SURFACE RELAXATIONLandau-type theories describe the observed behaviour of phase transitions in ferroelastic and co-elastic minerals and materials with a high degree of accuracy. In this review, the derivation of the Landau potential G = ½AθS [coth(θS/T) − coth(θS/TC)]Q2 + ¼BQ4 + … is derived as a solution of the general φ4 model. The coupling between the order parameter and spontaneous strain of a phase transition brings the behaviour of many phase transitions to the mean-field limit, even when the atomistic mechanism of the transition is spin-like. Strain coupling is also a common mechanism for the coupling between multiple order parameters in a single system. As well as changes on the crystal structure scale, phase transitions modify the microstructure of materials, leading to anomalous mesoscopic features at domain boundaries. The mesostructure of a domain wall is studied experimentally using X-ray diffraction, and interpreted theoretically using Ginzburg–Landau theory. One important consequence of twin mesostructures is their modified transport properties relative to the bulk. Domain wall motion also provides a mechanism for superelastic behaviour in ferroelastics. At surfaces, the relaxations that occur can be described in terms of order parameters and Landau theory. This leads to an exponential profile of surface relaxations. This in turn leads to an exponential interaction energy between surfaces, which can, if large enough, destabilize symmetrical morphologies in favour of a platelet morphology. Surface relaxations may also affect the behaviour of twin walls as they intersect surfaces, since the surface relaxation may lead to an incompatibility of the two domains at the surface, generating large strains at the relaxation. Landau theory may also be extended to describe the kinetics of phase transitions. Time-dependent Landau theory may be used to describe the kinetics of order–disorder phase transitions in which the order parameter is homogeneous. However, the time-dependent Landau theory equations also have microstructural solutions, explaining the formation of microstructures such as tweed.text/htmlFerroelastic phase transitions: structure and microstructuretext1612005-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2005 International Union of Crystallography0108-7673topical reviews3med@iucr.org181600-5724New information from modern charge density methods
http://scripts.iucr.org/cgi-bin/paper?me0264
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Larsen, F.K.2004-09-01doi:10.1107/S010876730402032XInternational Union of CrystallographyenPREFACE; CHARGE DENSITYtext/htmlNew information from modern charge density methodstext5602004-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673issue prefacemed@iucr.org1600-5724`In-situ' charge-density studies of photoinduced phenomena: possibilities for the future?
http://scripts.iucr.org/cgi-bin/paper?xc5020
Over the past decade, there has been much development in the structure determination of photoinduced species by single-crystal X-ray diffraction. Such work is key to understanding many photoactivated chemical processes and physical properties that are behind phenomena such as photoisomerism, photoinduced chemical reactions, light-induced spin-crossover transitions and molecular excited states that are responsible for many types of fluorescence and phosphorescence. A brief overview of these experimental developments is presented in relation to the attraction of conducting charge-density studies on photoinduced structures. The technical issues regarding possible charge-density studies using these developments, both in the metastable and time-resolved domain, are highlighted in the form of a perspective towards future possibilities for photoinduced charge-density studies. The paper concludes with a summary of further experimental developments that are unfolding and how these may contribute to the ultimate viability of `in-situ' charge-density studies on photoinduced phenomena.Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Cole, J.M.2004-09-01doi:10.1107/S0108767304017428International Union of CrystallographyThe experimental considerations required to obtain photoinduced crystal structures is described and related to the experimental and theoretical requirements of charge-density studies. The viability of combining these two experimental methodologies to realize a photoinduced charge-density study is explored.enCHARGE DENSITY; PHOTOINDUCED PHENOMENAOver the past decade, there has been much development in the structure determination of photoinduced species by single-crystal X-ray diffraction. Such work is key to understanding many photoactivated chemical processes and physical properties that are behind phenomena such as photoisomerism, photoinduced chemical reactions, light-induced spin-crossover transitions and molecular excited states that are responsible for many types of fluorescence and phosphorescence. A brief overview of these experimental developments is presented in relation to the attraction of conducting charge-density studies on photoinduced structures. The technical issues regarding possible charge-density studies using these developments, both in the metastable and time-resolved domain, are highlighted in the form of a perspective towards future possibilities for photoinduced charge-density studies. The paper concludes with a summary of further experimental developments that are unfolding and how these may contribute to the ultimate viability of `in-situ' charge-density studies on photoinduced phenomena.text/html`In-situ' charge-density studies of photoinduced phenomena: possibilities for the future?text5602004-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673research papers472med@iucr.org4791600-5724Coordinate transformations in modern crystallographic computing
http://scripts.iucr.org/cgi-bin/paper?gc0049
A review of 4 × 4-matrix notation and of tensor formalism focused on crystallographic applications is presented. A discussion of examples shows how this notation simplifies tasks encountered in crystallographic computing.Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Rowicka, M.Kudlicki, A.Zelinka, J.Otwinowski, Z.2004-11-01doi:10.1107/S0108767304017398International Union of CrystallographyA review of 4 × 4 matrix notation and of tensor formalism focused on crystallographic applications, including examples from crystallographic computing.enMATRIX NOTATION; TENSOR FORMALISM; COORDINATE TRANSFORMATIONSA review of 4 × 4-matrix notation and of tensor formalism focused on crystallographic applications is presented. A discussion of examples shows how this notation simplifies tasks encountered in crystallographic computing.text/htmlCoordinate transformations in modern crystallographic computingtext6602004-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673research papers542med@iucr.org5491600-5724The quantum topological electrostatic potential as a probe for functional group transferability
http://scripts.iucr.org/cgi-bin/paper?xc5015
The electrostatic potential can be used as an appropriate and convenient indicator of how transferable an atom or functional group is between two molecules. Quantum-chemical topology (QCT) is used to define the electron density of a molecular fragment and the electrostatic potential it generates. The potential generated on a grid by the terminal aldehyde group of the biomolecule retinal is compared with the corresponding aldehyde group in smaller molecules derived from retinal. The terminal amino group in the free amino acid lysine was treated in a similar fashion. Each molecule is geometry-optimized by an ab initio calculation at B3LYP/6-311G+(2d,p)//HF/6-31G(d) level. The amino group in lysine is very little influenced by any part of the molecule further than two C atoms away. However, the aldehyde group in retinal is influenced by molecular fragments six C atoms away. This dramatic disparity is ascribed to the difference in saturation in the carbon chains; retinal contains a conjugated hydrocarbon chain but lysine an aliphatic one.Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Popelier, P.L.A.Devereux, M.Rafat, M.2004-09-01doi:10.1107/S0108767304016228International Union of CrystallographyThe electrostatic potential can be used as an appropriate and convenient indicator of how transferable an atom or functional group is between two molecules. Quantum-chemical topology is used to define the electron density of a molecular fragment and the electrostatic potential it generates.enELECTRON DENSITY; QUANTUM-CHEMICAL TOPOLOGY; ELECTROSTATIC POTENTIAL; FUNCTIONAL GROUP TRANSFERABILITYThe electrostatic potential can be used as an appropriate and convenient indicator of how transferable an atom or functional group is between two molecules. Quantum-chemical topology (QCT) is used to define the electron density of a molecular fragment and the electrostatic potential it generates. The potential generated on a grid by the terminal aldehyde group of the biomolecule retinal is compared with the corresponding aldehyde group in smaller molecules derived from retinal. The terminal amino group in the free amino acid lysine was treated in a similar fashion. Each molecule is geometry-optimized by an ab initio calculation at B3LYP/6-311G+(2d,p)//HF/6-31G(d) level. The amino group in lysine is very little influenced by any part of the molecule further than two C atoms away. However, the aldehyde group in retinal is influenced by molecular fragments six C atoms away. This dramatic disparity is ascribed to the difference in saturation in the carbon chains; retinal contains a conjugated hydrocarbon chain but lysine an aliphatic one.text/htmlThe quantum topological electrostatic potential as a probe for functional group transferabilitytext5602004-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673research papers427med@iucr.org4331600-5724Response to the paper A comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large molecules, by Pichon-Pesme, Jelsch, Guillot & Lecomte (2004)
http://scripts.iucr.org/cgi-bin/paper?sh0179
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Volkov, A.Koritsanszky, T.Li, X.Coppens, P.2004-11-01doi:10.1107/S0108767304016496International Union of CrystallographyComment on Pichon-Pesme et al. [Acta Cryst. (2004), A60, 204–208].enCHARGE DENSITY; ELECTRON DENSITY; POLYPEPTIDES; MACROMOLECULAR CRYSTALLOGRAPHY; PROTEIN CRYSTALLOGRAPHY; DATABASEtext/htmlResponse to the paper A comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large molecules, by Pichon-Pesme, Jelsch, Guillot & Lecomte (2004)text6602004-11-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673letters to the editor638med@iucr.org6391600-5724On the role of data quality in experimental charge-density studies
http://scripts.iucr.org/cgi-bin/paper?xc5014
High-resolution X-ray diffraction data were collected at T = 19 K from two similar spherical crystals of the fungal metabolite citrinin, C13H14O5. The two data sets were of markedly different quality, one data set (MQ, medium quality) comprising a single octant of the reciprocal lattice and including reflections with obviously peculiar intensity profiles while the second (HQ, high quality) comprised a hemisphere of reflections and showed no flawed profiles. Parallel multipolar refinements were carried out for both. While most of the resulting geometric parameters, including bond lengths and angles, were in close agreement (the standard uncertainties were approximately twice as large for the MQ data, reflecting the smaller number of observations), the agreement is noticeably worse for electronic properties such as electron densities and their Laplacians at the bond and ring critical points. These latter features are especially sensitive to the quality of the low-angle (and strong) intensities, which was not high for the MQ data. By contrast, the magnitudes of the molecular dipole moment from the two experiments are the same within 1 standard uncertainty, with an angle of about 13° between the two vectors. It is concluded that only true high-quality data allow a fully significant and quantitative analysis of the details of the experimental electron density ρexp, while high-resolution medium-quality data, measured at very low temperature and adequately processed, can still be used for a qualitative analysis, or for the derivation of overall electronic properties.Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Destro, R.Loconte, L.Lo Presti, L.Roversi, P.Soave, R.2004-09-01doi:10.1107/S0108767304014813International Union of CrystallographyElectron distributions from multipolar refinement of two sets of high-resolution X-ray diffraction data of different quality, measured at T = 19 K from two different spherical crystals of the same compound, are analysed and compared.enELECTRON DENSITY; TOPOLOGICAL ANALYSIS; MOLECULAR ELECTRIC MOMENTS; DATA QUALITYHigh-resolution X-ray diffraction data were collected at T = 19 K from two similar spherical crystals of the fungal metabolite citrinin, C13H14O5. The two data sets were of markedly different quality, one data set (MQ, medium quality) comprising a single octant of the reciprocal lattice and including reflections with obviously peculiar intensity profiles while the second (HQ, high quality) comprised a hemisphere of reflections and showed no flawed profiles. Parallel multipolar refinements were carried out for both. While most of the resulting geometric parameters, including bond lengths and angles, were in close agreement (the standard uncertainties were approximately twice as large for the MQ data, reflecting the smaller number of observations), the agreement is noticeably worse for electronic properties such as electron densities and their Laplacians at the bond and ring critical points. These latter features are especially sensitive to the quality of the low-angle (and strong) intensities, which was not high for the MQ data. By contrast, the magnitudes of the molecular dipole moment from the two experiments are the same within 1 standard uncertainty, with an angle of about 13° between the two vectors. It is concluded that only true high-quality data allow a fully significant and quantitative analysis of the details of the experimental electron density ρexp, while high-resolution medium-quality data, measured at very low temperature and adequately processed, can still be used for a qualitative analysis, or for the derivation of overall electronic properties.text/htmlOn the role of data quality in experimental charge-density studiestext5602004-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673research papers365med@iucr.org3701600-5724U4O9: atoms in general sites giving the hkl extinctions of special sites
http://scripts.iucr.org/cgi-bin/paper?lc0065
In U4O9, most of the atoms are in general 48-fold [48(e)] sites of the space group I\bar43d and yet the hkl reflections obey the extinction rules for atoms occupying special 12-fold [12(b)] sites. An explanation is given for this effect, which can be generalized to any space group.Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Popa, N.C.Willis, B.T.M.2004-07-01doi:10.1107/S0108767304012188International Union of CrystallographyIn U4O9, the hkl reflections obey the extinction rules for atoms occupying special 12-fold [12(b) of space group I\bar43d] sites. An explanation is given for this effect, which can be generalized to any space group.enSPECIAL REFLECTION CONDITIONS; URANIUM OXIDE; SYSTEMATIC ABSENCESIn U4O9, most of the atoms are in general 48-fold [48(e)] sites of the space group I\bar43d and yet the hkl reflections obey the extinction rules for atoms occupying special 12-fold [12(b)] sites. An explanation is given for this effect, which can be generalized to any space group.text/htmlU4O9: atoms in general sites giving the hkl extinctions of special sitestext4602004-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673research papers318med@iucr.org3211600-5724Refinement of the structure of β-U4O9
http://scripts.iucr.org/cgi-bin/paper?lc0066
β-U4O9 is a superlattice structure based on the fluorite arrangement of UO2. The U atoms occupy positions close to those in UO2 and the additional O atoms are accommodated in cuboctahedral clusters of \bar43m symmetry, which are centred on the special 12-fold sites of the cubic space group I\bar43d. The structure has been refined from single-crystal neutron data in accordance with the procedure described in the previous paper [Popa & Willis (2004). Acta Cryst. A60, 318–321].Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Cooper, R.I.Willis, B.T.M.2004-07-01doi:10.1107/S010876730401219XInternational Union of CrystallographyThe structure of β-U4O9 has been refined from single-crystal neutron data in the space group I\bar43d taking into account the findings described in the previous paper.enCLUSTERS; URANIUM OXIDE; NEUTRON SCATTERINGβ-U4O9 is a superlattice structure based on the fluorite arrangement of UO2. The U atoms occupy positions close to those in UO2 and the additional O atoms are accommodated in cuboctahedral clusters of \bar43m symmetry, which are centred on the special 12-fold sites of the cubic space group I\bar43d. The structure has been refined from single-crystal neutron data in accordance with the procedure described in the previous paper [Popa & Willis (2004). Acta Cryst. A60, 318–321].text/htmlRefinement of the structure of β-U4O9text4602004-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673research papers322med@iucr.org3251600-5724Quantum Crystallography: Electron Density and Bonding, a Microsymposium
http://scripts.iucr.org/cgi-bin/paper?me0246
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Manninen, S.2004-03-01doi:10.1107/S0108767304002788International Union of CrystallographyenQUANTUM CRYSTALLOGRAPHYtext/htmlQuantum Crystallography: Electron Density and Bonding, a Microsymposiumtext2602004-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673topical reviews103med@iucr.org1031600-5724Nominations for the Ewald Prize
http://scripts.iucr.org/cgi-bin/paper?es0334
Copyright (c) 2004 International Union of Crystallographyurn:issn:0108-7673Duax, W.L.Larsen, S.2004-01-01doi:10.1107/S0108767303028964International Union of Crystallographyentext/htmlNominations for the Ewald Prizetext1602004-01-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2004 International Union of Crystallography0108-7673international union of crystallography96med@iucr.org961600-5724The maximum-entropy method in superspace
http://scripts.iucr.org/cgi-bin/paper?lc0060
One of the applications of the maximum-entropy method (MEM) in crystallography is the reconstruction of the electron density from phased structure factors. Here the application of the MEM to incommensurately modulated crystals and incommensurate composite crystals is considered. The MEM is computed directly in superspace, where the electron density in the (3+d)-dimensional unit cell (d > 0) is determined from the scattering data of aperiodic crystals. Periodic crystals (d = 0) are treated as a special case of the general formalism. The use of symmetry in the MEM is discussed and an efficient algorithm is proposed for handling crystal symmetry. The method has been implemented into a computer program BayMEM and applications are presented to the electron density of the periodic crystal NaV2O5 and the electron density of the incommensurate composite crystal (LaS)1.14NbS2. The MEM in superspace is shown to provide a model-independent estimate of the shapes of the modulation functions of incommensurate crystals. The discrete character of the electron density is found to be the major source of error, limiting the accuracy of the reconstructed modulation functions to approximately 10% of the sizes of the pixels. MaxEnt optimization using the Cambridge and Sakata–Sato algorithms are compared. The Cambridge algorithm is found to perform better than the Sakata–Sato algorithm, being faster, always reaching convergence, and leading to more reliable density maps. Nevertheless, the Sakata–Sato algorithm leads to similar density maps, even in cases where it does not reach complete convergence.Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Smaalen, S. vanPalatinus, L.Schneider, M.2003-09-01doi:10.1107/S010876730301434XInternational Union of CrystallographyThe maximum-entropy method (MEM) for the analysis of the electron densities of periodic and aperiodic crystals is critically evaluated. It is shown that the MEM in superspace provides a model-independent reconstruction of the shapes of the modulation functions of incommensurate crystals.enMAXIMUM-ENTROPY METHOD; APERIODIC CRYSTALS; ELECTRON DENSITYOne of the applications of the maximum-entropy method (MEM) in crystallography is the reconstruction of the electron density from phased structure factors. Here the application of the MEM to incommensurately modulated crystals and incommensurate composite crystals is considered. The MEM is computed directly in superspace, where the electron density in the (3+d)-dimensional unit cell (d > 0) is determined from the scattering data of aperiodic crystals. Periodic crystals (d = 0) are treated as a special case of the general formalism. The use of symmetry in the MEM is discussed and an efficient algorithm is proposed for handling crystal symmetry. The method has been implemented into a computer program BayMEM and applications are presented to the electron density of the periodic crystal NaV2O5 and the electron density of the incommensurate composite crystal (LaS)1.14NbS2. The MEM in superspace is shown to provide a model-independent estimate of the shapes of the modulation functions of incommensurate crystals. The discrete character of the electron density is found to be the major source of error, limiting the accuracy of the reconstructed modulation functions to approximately 10% of the sizes of the pixels. MaxEnt optimization using the Cambridge and Sakata–Sato algorithms are compared. The Cambridge algorithm is found to perform better than the Sakata–Sato algorithm, being faster, always reaching convergence, and leading to more reliable density maps. Nevertheless, the Sakata–Sato algorithm leads to similar density maps, even in cases where it does not reach complete convergence.text/htmlThe maximum-entropy method in superspacetext5592003-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673research papers459med@iucr.org4691600-5724High-resolution electron microscopy. 3rd edition. By John C. H. Spence. Pp. xvi + 401. Oxford University Press, 2003. Price GBP 69.95. ISBN 0-19-850915-4.
http://scripts.iucr.org/cgi-bin/paper?ht5045
Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Vincent, R.2003-09-01doi:10.1107/S010876730301300XInternational Union of CrystallographyenBOOK REVIEWtext/htmlHigh-resolution electron microscopy. 3rd edition. By John C. H. Spence. Pp. xvi + 401. Oxford University Press, 2003. Price GBP 69.95. ISBN 0-19-850915-4.text5592003-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673book reviews513med@iucr.org5141600-5724On quaternions and octonions: their geometry, arithmetic and symmetry. By John H. Conway and Derek A. Smith. Natick, MA: A. K. Peters Ltd, 2003. Price USD 29.00. ISBN 1-56881-134-9
http://scripts.iucr.org/cgi-bin/paper?ht5040
Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Grimmer, H.2003-07-01doi:10.1107/S0108767303010870International Union of Crystallographyentext/htmlOn quaternions and octonions: their geometry, arithmetic and symmetry. By John H. Conway and Derek A. Smith. Natick, MA: A. K. Peters Ltd, 2003. Price USD 29.00. ISBN 1-56881-134-9text4592003-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673book reviews436med@iucr.org4361600-5724Linus Pauling selected scientific papers. Edited by Barclay Kamb, Linda Pauling Kamb, Peter Jeffress Pauling, Alexander Kamb and Linus Pauling Jr. Singapore: World Scientific, 2001. Vols. 1 and 2 set: 1612 pp., USD 114, ISBN 981-02-2784-1; Vol. 1: 864 pp., USD 98, ISBN 981-02-2939-9; Vol. 2: 748 pp., USD 67, ISBN 981-02-2940-2.
http://scripts.iucr.org/cgi-bin/paper?ht5003
Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Thomas, J.M.2003-07-01doi:10.1107/S0108767303010845International Union of Crystallographyentext/htmlLinus Pauling selected scientific papers. Edited by Barclay Kamb, Linda Pauling Kamb, Peter Jeffress Pauling, Alexander Kamb and Linus Pauling Jr. Singapore: World Scientific, 2001. Vols. 1 and 2 set: 1612 pp., USD 114, ISBN 981-02-2784-1; Vol. 1: 864 pp., USD 98, ISBN 981-02-2939-9; Vol. 2: 748 pp., USD 67, ISBN 981-02-2940-2.text4592003-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673book reviews434med@iucr.org4361600-5724Structure, odd lines and topological entropy of disorder of amorphous silicon. Correction
http://scripts.iucr.org/cgi-bin/paper?bk9109
Wooten [Acta Cryst. (2002), A58, 346–351] defines cells in amorphous Si as being bounded by irreducible rings of atoms, which can be viewed as distorted polygons. These irreducible rings are, roughly speaking, shortest rings. However, the definition used is incomplete and leads to some large rings being counted as irreducible when close examination reveals they are not. In particular, the incomplete definition counts four ninefold rings (out of a total of 1041 ninefold rings) as being irreducible. Yet a detailed examination reveals that these four rings bound a set of smaller rings, and are clearly not irreducible in any meaningful sense of the word. An extended definition has been given [Rivier & Wooten (2003). MATCH – Commun. Math. Comput. Chem. 48, 145–153], and described at length, that removes the difficulties. It results in a small increase in entropy, approaching slightly closer to the ideal. The first paragraph of Wooten (2002) incorrectly states that the nearest-neighbor distance in Si is 3.5 Å, rather than the correct value of 2.35 Å. This misprint has no effect on anything else.Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Wooten, F.2003-05-01doi:10.1107/S0108767303007037International Union of CrystallographyErratum to Acta Cryst. (2002), A58, 346–351.enENTROPY; AMORPHOUS SILICON; DISORDERWooten [Acta Cryst. (2002), A58, 346–351] defines cells in amorphous Si as being bounded by irreducible rings of atoms, which can be viewed as distorted polygons. These irreducible rings are, roughly speaking, shortest rings. However, the definition used is incomplete and leads to some large rings being counted as irreducible when close examination reveals they are not. In particular, the incomplete definition counts four ninefold rings (out of a total of 1041 ninefold rings) as being irreducible. Yet a detailed examination reveals that these four rings bound a set of smaller rings, and are clearly not irreducible in any meaningful sense of the word. An extended definition has been given [Rivier & Wooten (2003). MATCH – Commun. Math. Comput. Chem. 48, 145–153], and described at length, that removes the difficulties. It results in a small increase in entropy, approaching slightly closer to the ideal. The first paragraph of Wooten (2002) incorrectly states that the nearest-neighbor distance in Si is 3.5 Å, rather than the correct value of 2.35 Å. This misprint has no effect on anything else.text/htmlStructure, odd lines and topological entropy of disorder of amorphous silicon. Correctiontext3592003-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673addenda and errata286med@iucr.org2861600-5724Multiparametric scaling of diffraction intensities
http://scripts.iucr.org/cgi-bin/paper?we0011
A novel and general approach to scaling diffraction intensities is presented. The method minimizes the disagreement among multiple measurements of symmetry-related reflections using a stable refinement procedure. The scale factors are described by a flexible exponential function that allows different scaling corrections to be chosen and combined according to the needs of the experiment. The scaling model presented here includes: scale and temperature factor per batch of data; temperature factor as a continuous function of the radiation dose; absorption in the crystal; uneven exposure within a single diffraction image; and corrections for phenomena that depend on the diffraction peak position on the detector. This scaling model can be extended to include additional corrections for various instrumental and data-collection problems.Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Otwinowski, Z.Borek, D.Majewski, W.Minor, W.2003-05-01doi:10.1107/S0108767303005488International Union of CrystallographyA novel method of scaling diffraction intensities is presented.enSCALING; ABSORPTION; DIFFRACTION; EXPONENTIAL MODELLINGA novel and general approach to scaling diffraction intensities is presented. The method minimizes the disagreement among multiple measurements of symmetry-related reflections using a stable refinement procedure. The scale factors are described by a flexible exponential function that allows different scaling corrections to be chosen and combined according to the needs of the experiment. The scaling model presented here includes: scale and temperature factor per batch of data; temperature factor as a continuous function of the radiation dose; absorption in the crystal; uneven exposure within a single diffraction image; and corrections for phenomena that depend on the diffraction peak position on the detector. This scaling model can be extended to include additional corrections for various instrumental and data-collection problems.text/htmlMultiparametric scaling of diffraction intensitiestext3592003-05-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673research papers228med@iucr.org2341600-5724The physics of ferroelectric and antiferroelectric liquid crystals. By I. Musevic, R. Blinc & B. Zeks. Singapore: World Scientific, 2000. Pp. 680. USD 129, GBP 88. ISBN 981-02-0325-X
http://scripts.iucr.org/cgi-bin/paper?ht5027
Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Hart, M.2003-09-01doi:10.1107/S0108767303004719International Union of CrystallographyenBOOK RECEIVEDtext/htmlThe physics of ferroelectric and antiferroelectric liquid crystals. By I. Musevic, R. Blinc & B. Zeks. Singapore: World Scientific, 2000. Pp. 680. USD 129, GBP 88. ISBN 981-02-0325-Xtext5592003-09-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673books received514med@iucr.org5141600-5724A new method for calculation of crystal susceptibilities for X-ray diffraction at arbitrary wavelength. Erratum
http://scripts.iucr.org/cgi-bin/paper?we9009
In the paper by Feranchuk, Gurskii, Komarov, Lugovskaya, Burgäzy & Ulyanenkov [Acta Cryst. (2002). A58, 370–384], there is a misprint in equation (22): instead of parameter s, the normalized parameter s1 = 4πa0s has to be used, where a0 = 0.529177 Å is a Bohr radius. The conclusions and other results are correct.Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Feranchuk, I.D.Gurskii, L.I.Komarov, L.I.Lugovskaya, O.M.Burgäzy, F.Ulyanenkov, A.2003-03-01doi:10.1107/S0108767303002216International Union of CrystallographyErratum to Acta Cryst. A58, 370–384.enSUSCEPTIBILITY; ATOMIC SCATTERING FACTOR; DEBYE-WALLER FACTORIn the paper by Feranchuk, Gurskii, Komarov, Lugovskaya, Burgäzy & Ulyanenkov [Acta Cryst. (2002). A58, 370–384], there is a misprint in equation (22): instead of parameter s, the normalized parameter s1 = 4πa0s has to be used, where a0 = 0.529177 Å is a Bohr radius. The conclusions and other results are correct.text/htmlA new method for calculation of crystal susceptibilities for X-ray diffraction at arbitrary wavelength. Erratumtext2592003-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673addenda and errata199med@iucr.org1991600-5724Quasicrystals. The state of the art. (2nd ed.) Edited by D. P. Vincenzo and P. J. Steinhardt. Series on Directions in Condensed Matter Physics, Vol. 16. Pp. xi + 618. Singapore: World Scientific, 1999. Price (hardback) USD 113, GBP 71, ISBN 981-02-4155-0; (paperback) USD 55, GBP 34, ISBN 981-02-4156-9.
http://scripts.iucr.org/cgi-bin/paper?ht5009
Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Steurer, W.2003-07-01doi:10.1107/S0108767303001697International Union of Crystallographyentext/htmlQuasicrystals. The state of the art. (2nd ed.) Edited by D. P. Vincenzo and P. J. Steinhardt. Series on Directions in Condensed Matter Physics, Vol. 16. Pp. xi + 618. Singapore: World Scientific, 1999. Price (hardback) USD 113, GBP 71, ISBN 981-02-4155-0; (paperback) USD 55, GBP 34, ISBN 981-02-4156-9.text4592003-07-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673book reviews434med@iucr.org4341600-5724Fundamentals of crystallography, 2nd edition. Edited by C. Giacovazzo. IUCr Texts on Crystallography 7. Oxford: IUCr/Oxford University Press, 2002. Pp. xxi + 825 + included CD. Price (hardback) GBP 75.00, ISBN 0-19-850957-X; (paperback) GBP 39.50, ISBN 0-19-850958-8.
http://scripts.iucr.org/cgi-bin/paper?ht5000
Copyright (c) 2003 International Union of Crystallographyurn:issn:0108-7673Bryan, R.F.2003-03-01doi:10.1107/S0108767302020238International Union of CrystallographyenBOOK REVIEWtext/htmlFundamentals of crystallography, 2nd edition. Edited by C. Giacovazzo. IUCr Texts on Crystallography 7. Oxford: IUCr/Oxford University Press, 2002. Pp. xxi + 825 + included CD. Price (hardback) GBP 75.00, ISBN 0-19-850957-X; (paperback) GBP 39.50, ISBN 0-19-850958-8.text2592003-03-01Acta Crystallographica Section A: Foundations of CrystallographyCopyright (c) 2003 International Union of Crystallography0108-7673book reviews200med@iucr.org2001600-5724