Open-access and free articles in Journal of Applied Crystallography
https://journals.iucr.org/j/journalhomepage.html
Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.en-gbCopyright (c) 2018 International Union of CrystallographyInternational Union of CrystallographyInternational Union of Crystallographyhttps://journals.iucr.orgurn:issn:0021-8898Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.text/htmlOpen-access and free articles in Journal of Applied Crystallographytextyearly62002-02-01T00:00+00:00med@iucr.orgJournal of Applied CrystallographyCopyright (c) 2018 International Union of Crystallographyurn:issn:0021-8898Open-access and free articles in Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gif
https://journals.iucr.org/j/journalhomepage.html
Still imageThe high-intensity option of the SANS diffractometer KWS-2 at JCNS – characterization and performance of the new multi-megahertz detection system
http://scripts.iucr.org/cgi-bin/paper?uj5002
A new detection system based on an array of 3He tubes and innovative fast detection electronics has been installed on the high-intensity small-angle neutron scattering (SANS) diffractometer KWS-2 operated by the Jülich Centre for Neutron Science (JCNS) at the Heinz Meier-Leibnitz Zentrum in Garching, Germany. The new detection system is composed of 18 eight-pack modules of 3He tubes that work independently of one another (each unit has its own processor and electronics). To improve the read-out characteristics and reduce the noise, the detection electronics are mounted in a closed case on the rear of the 3He tubes' frame. The tubes' efficiency is about 85% (for λ = 5 Å) and the resolution slightly better than 8 mm. The new detection system is characterized by a dead-time constant of 3.3 µs per tube and an overall count rate as high as 6 MHz at 10% dead-time loss. Compared with the old detector this is an improvement by a factor of 60. The much higher count rate will shorten the measurement times and thus increase the number of experiments possible in a given time period by the optimal use of the high flux of up to 2 × 108 n cm−2 s−1 at the sample position. Combined with the event-mode operation capability, this will enable new scientific opportunities in the field of structural investigations of small soft-matter and biological systems. The implementation of the detector in the high-intensity concept on KWS-2, its characterization and its performance based on test experiments are reported in this paper.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Houston, J.E.Brandl, G.Drochner, M.Kemmerling, G.Engels, R.Papagiannopoulos, A.Sarter, M.Stadler, A.Radulescu, A.2018-03-28doi:10.1107/S1600576718004132International Union of CrystallographyA new detection system based on an array of 3He tubes and innovative fast detection electronics has been installed on the small-angle neutron scattering (SANS) diffractometer KWS-2 at the Jülich Centre for Neutron Science (JCNS), Germany. The high counting rates that can be detected and the event-mode capability will enable new scientific opportunities in the field of structural investigation of small soft-matter and biological systems.enSMALL-ANGLE NEUTRON SCATTERING (SANS); NEUTRON DETECTORS; MESOSCALE STRUCTURES; EVENT-MODE CAPABILITYA new detection system based on an array of 3He tubes and innovative fast detection electronics has been installed on the high-intensity small-angle neutron scattering (SANS) diffractometer KWS-2 operated by the Jülich Centre for Neutron Science (JCNS) at the Heinz Meier-Leibnitz Zentrum in Garching, Germany. The new detection system is composed of 18 eight-pack modules of 3He tubes that work independently of one another (each unit has its own processor and electronics). To improve the read-out characteristics and reduce the noise, the detection electronics are mounted in a closed case on the rear of the 3He tubes' frame. The tubes' efficiency is about 85% (for λ = 5 Å) and the resolution slightly better than 8 mm. The new detection system is characterized by a dead-time constant of 3.3 µs per tube and an overall count rate as high as 6 MHz at 10% dead-time loss. Compared with the old detector this is an improvement by a factor of 60. The much higher count rate will shorten the measurement times and thus increase the number of experiments possible in a given time period by the optimal use of the high flux of up to 2 × 108 n cm−2 s−1 at the sample position. Combined with the event-mode operation capability, this will enable new scientific opportunities in the field of structural investigations of small soft-matter and biological systems. The implementation of the detector in the high-intensity concept on KWS-2, its characterization and its performance based on test experiments are reported in this paper.text/htmlThe high-intensity option of the SANS diffractometer KWS-2 at JCNS – characterization and performance of the new multi-megahertz detection systemtext2512018-03-28Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers323med@iucr.orgApril 20183361600-5767Implementation of cross correlation for energy discrimination on the time-of-flight spectrometer CORELLI
http://scripts.iucr.org/cgi-bin/paper?ut5001
The CORELLI instrument at Oak Ridge National Laboratory is a statistical chopper spectrometer designed and optimized to probe complex disorder in crystalline materials through diffuse scattering experiments. On CORELLI, the high efficiency of white-beam Laue diffraction combined with elastic discrimination have enabled an unprecedented data collection rate to obtain both the total and the elastic-only scattering over a large volume of reciprocal space from a single measurement. To achieve this, CORELLI is equipped with a statistical chopper to modulate the incoming neutron beam quasi-randomly, and then the cross-correlation method is applied to reconstruct the elastic component from the scattering data. Details of the implementation of the cross-correlation method on CORELLI are given and its performance is discussed.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ye, F.Liu, Y.Whitfield, R.Osborn, R.Rosenkranz, S.2018-03-26doi:10.1107/S160057671800403XInternational Union of CrystallographyWith implementation of the cross-correlation technique at the short-pulse Spallation Neutron Source (SNS), Oak Ridge, Tennessee, USA, CORELLI obtains both the total scattering and the elastic-only scattering simultaneously from a single measurement with an unprecedented data collection rate.enNEUTRON DIFFRACTION; ENERGY DISCRIMINATION; CROSS-CORRELATION TECHNIQUE; TIME-OF-FLIGHT NEUTRON BEAMLINESThe CORELLI instrument at Oak Ridge National Laboratory is a statistical chopper spectrometer designed and optimized to probe complex disorder in crystalline materials through diffuse scattering experiments. On CORELLI, the high efficiency of white-beam Laue diffraction combined with elastic discrimination have enabled an unprecedented data collection rate to obtain both the total and the elastic-only scattering over a large volume of reciprocal space from a single measurement. To achieve this, CORELLI is equipped with a statistical chopper to modulate the incoming neutron beam quasi-randomly, and then the cross-correlation method is applied to reconstruct the elastic component from the scattering data. Details of the implementation of the cross-correlation method on CORELLI are given and its performance is discussed.text/htmlImplementation of cross correlation for energy discrimination on the time-of-flight spectrometer CORELLItext2512018-03-26Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers315med@iucr.orgApril 20183221600-5767RABDAM: quantifying specific radiation damage in individual protein crystal structures
http://scripts.iucr.org/cgi-bin/paper?ap5024
Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of the BDamage metric has helped to address this problem. BDamage is a quantitative, per-atom metric identifies potential sites of specific damage by comparing the atomic B-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program, RABDAM, to calculate the BDamage metric for all selected atoms within any standard-format PDB or mmCIF file. RABDAM provides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Shelley, K.L.Dixon, T.P.E.Brooks-Bartlett, J.C.Garman, E.F.2018-03-28doi:10.1107/S1600576718002509International Union of CrystallographyA program to measure the extent of specific radiation damage suffered by an individual protein crystal structure, suitable for running on any standard-format PDB or mmCIF file, is presented.enRADIATION DAMAGE; ATOMIC B FACTORS; ATOMIC DISPLACEMENT PARAMETERS; BDAMAGE; RABDAM; PROTEIN DATA BANK; PDB; PROTEIN CRYSTALLOGRAPHY; COMPUTER PROGRAMSRadiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of the BDamage metric has helped to address this problem. BDamage is a quantitative, per-atom metric identifies potential sites of specific damage by comparing the atomic B-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program, RABDAM, to calculate the BDamage metric for all selected atoms within any standard-format PDB or mmCIF file. RABDAM provides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.text/htmlRABDAM: quantifying specific radiation damage in individual protein crystal structurestext2512018-03-28Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs552med@iucr.orgApril 20185591600-5767Optimization of moderators and beam extraction at the ESS
http://scripts.iucr.org/cgi-bin/paper?uh5002
A global approach coupling the moderator to the beam extraction system has been applied for the design optimization of the thermal and cold moderators of the European Spallation Source (ESS), which will be the brightest neutron source in the world for condensed-matter studies. The design is based on the recently developed high-brightness low-dimensional moderator concepts. Para-hydrogen is used for the cold neutron source, while thermal neutrons are provided by moderation in water. The overall moderation configuration was chosen in order to satisfy a range of requirements on bispectral extraction, beamport configuration and instrument performance. All instruments are served by a single moderator assembly above the target, arranged in a `butterfly' geometry with a height of 3 cm. This was determined to be the optimal height for trade-off between high brightness and efficient guide illumination, by analysis of the performance of 23 instruments, based on the reference suite of the ESS Technical Design Report. The concept of `brilliance transfer' is introduced to quantify the performance of the neutron optical system from the source to the sample. The target monolith incorporates a grid of 42 neutron beamports with an average separation of 6°, allowing a free choice between cold and thermal neutron sources at all instrument positions. With the large number of beamports and the space below the target available for future moderators, ample opportunities are available for future upgrades.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Andersen, K.H.Bertelsen, M.Zanini, L.Klinkby, E.B.Schönfeldt, T.Bentley, P.M.Saroun, J.2018-03-12doi:10.1107/S1600576718002406International Union of CrystallographyAll instruments at the European Spallation Source (ESS), Lund, Sweden, are served by a carefully optimized moderator assembly, providing world-leading performance and excellent flexibility and upgradeability.enWATER MODERATORS; PARA-HYDROGEN MODERATORS; LOW-DIMENSIONAL MODERATORS; PANCAKE MODERATORS; BUTTERFLY MODERATORS; BRILLIANCE TRANSFER; NEUTRON INSTRUMENTSA global approach coupling the moderator to the beam extraction system has been applied for the design optimization of the thermal and cold moderators of the European Spallation Source (ESS), which will be the brightest neutron source in the world for condensed-matter studies. The design is based on the recently developed high-brightness low-dimensional moderator concepts. Para-hydrogen is used for the cold neutron source, while thermal neutrons are provided by moderation in water. The overall moderation configuration was chosen in order to satisfy a range of requirements on bispectral extraction, beamport configuration and instrument performance. All instruments are served by a single moderator assembly above the target, arranged in a `butterfly' geometry with a height of 3 cm. This was determined to be the optimal height for trade-off between high brightness and efficient guide illumination, by analysis of the performance of 23 instruments, based on the reference suite of the ESS Technical Design Report. The concept of `brilliance transfer' is introduced to quantify the performance of the neutron optical system from the source to the sample. The target monolith incorporates a grid of 42 neutron beamports with an average separation of 6°, allowing a free choice between cold and thermal neutron sources at all instrument positions. With the large number of beamports and the space below the target available for future moderators, ample opportunities are available for future upgrades.text/htmlOptimization of moderators and beam extraction at the ESStext2512018-03-12Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers264med@iucr.orgApril 20182811600-5767The thermal expansion of gold: point defect concentrations and pre-melting in a face-centred cubic metal
http://scripts.iucr.org/cgi-bin/paper?ks5577
On the basis of ab initio computer simulations, pre-melting phenomena have been suggested to occur in the elastic properties of hexagonal close-packed iron under the conditions of the Earth's inner core just before melting. The extent to which these pre-melting effects might also occur in the physical properties of face-centred cubic metals has been investigated here under more experimentally accessible conditions for gold, allowing for comparison with future computer simulations of this material. The thermal expansion of gold has been determined by X-ray powder diffraction from 40 K up to the melting point (1337 K). For the entire temperature range investigated, the unit-cell volume can be represented in the following way: a second-order Grüneisen approximation to the zero-pressure volumetric equation of state, with the internal energy calculated via a Debye model, is used to represent the thermal expansion of the `perfect crystal'. Gold shows a nonlinear increase in thermal expansion that departs from this Grüneisen–Debye model prior to melting, which is probably a result of the generation of point defects over a large range of temperatures, beginning at T/Tm > 0.75 (a similar homologous T to where softening has been observed in the elastic moduli of Au). Therefore, the thermodynamic theory of point defects was used to include the additional volume of the vacancies at high temperatures (`real crystal'), resulting in the following fitted parameters: Q = (V0K0)/γ = 4.04 (1) × 10−18 J, V0 = 67.1671 (3) Å3, b = (K0′ − 1)/2 = 3.84 (9), θD = 182 (2) K, (vf/Ω)exp(sf/kB) = 1.8 (23) and hf = 0.9 (2) eV, where V0 is the unit-cell volume at 0 K, K0 and K0′ are the isothermal incompressibility and its first derivative with respect to pressure (evaluated at zero pressure), γ is a Grüneisen parameter, θD is the Debye temperature, vf, hf and sf are the vacancy formation volume, enthalpy and entropy, respectively, Ω is the average volume per atom, and kB is Boltzmann's constant.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Pamato, M.G.Wood, I.G.Dobson, D.P.Hunt, S.A.Vočadlo, L.2018-03-26doi:10.1107/S1600576718002248International Union of CrystallographyThe thermal expansion of gold has been determined by X-ray powder diffraction from 40 K up to the melting point (1337 K). Gold shows a nonlinear increase in thermal expansion that departs from the associated Grüneisen–Debye model prior to melting, which has been quantified in terms of the generation of point defects.enPRE-MELTING PHENOMENA; THERMAL EXPANSION; GOLD; VACANCIESOn the basis of ab initio computer simulations, pre-melting phenomena have been suggested to occur in the elastic properties of hexagonal close-packed iron under the conditions of the Earth's inner core just before melting. The extent to which these pre-melting effects might also occur in the physical properties of face-centred cubic metals has been investigated here under more experimentally accessible conditions for gold, allowing for comparison with future computer simulations of this material. The thermal expansion of gold has been determined by X-ray powder diffraction from 40 K up to the melting point (1337 K). For the entire temperature range investigated, the unit-cell volume can be represented in the following way: a second-order Grüneisen approximation to the zero-pressure volumetric equation of state, with the internal energy calculated via a Debye model, is used to represent the thermal expansion of the `perfect crystal'. Gold shows a nonlinear increase in thermal expansion that departs from this Grüneisen–Debye model prior to melting, which is probably a result of the generation of point defects over a large range of temperatures, beginning at T/Tm > 0.75 (a similar homologous T to where softening has been observed in the elastic moduli of Au). Therefore, the thermodynamic theory of point defects was used to include the additional volume of the vacancies at high temperatures (`real crystal'), resulting in the following fitted parameters: Q = (V0K0)/γ = 4.04 (1) × 10−18 J, V0 = 67.1671 (3) Å3, b = (K0′ − 1)/2 = 3.84 (9), θD = 182 (2) K, (vf/Ω)exp(sf/kB) = 1.8 (23) and hf = 0.9 (2) eV, where V0 is the unit-cell volume at 0 K, K0 and K0′ are the isothermal incompressibility and its first derivative with respect to pressure (evaluated at zero pressure), γ is a Grüneisen parameter, θD is the Debye temperature, vf, hf and sf are the vacancy formation volume, enthalpy and entropy, respectively, Ω is the average volume per atom, and kB is Boltzmann's constant.text/htmlThe thermal expansion of gold: point defect concentrations and pre-melting in a face-centred cubic metaltext2512018-03-26Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers470med@iucr.orgApril 20184801600-5767System for in situ observation of three-dimensional structural changes in polymer films during uniaxial deformation. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?fs5157
Ambiguities in the article by Miyazaki, Shimokita, Ogawa & Yamamoto [J. Appl. Cryst. (2015), 48, 1016–1022] are clarified.Copyright (c) 2018 International Union of Crystallographyurn:issn:1600-5767Miyazaki, T.Shimokita, K.Ogawa, H.Yamamoto, K.2018-02-06doi:10.1107/S1600576718001875International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2015), 48, 1016–1022.enSMALL-ANGLE X-RAY SCATTERING; WIDE-ANGLE X-RAY DIFFRACTION; STRESS-STRAIN RELATIONSHIPS; THREE-DIMENSIONAL STRUCTURAL EVALUATIONAmbiguities in the article by Miyazaki, Shimokita, Ogawa & Yamamoto [J. Appl. Cryst. (2015), 48, 1016–1022] are clarified.text/htmlSystem for in situ observation of three-dimensional structural changes in polymer films during uniaxial deformation. Corrigendumtext2512018-02-06Journal of Applied CrystallographyCopyright (c) 2018 International Union of Crystallography1600-5767addenda and errata560med@iucr.orgApril 20185611600-5767A Monte Carlo approach for scattering correction towards quantitative neutron imaging of polycrystals
http://scripts.iucr.org/cgi-bin/paper?po5111
The development of neutron imaging from a qualitative inspection tool towards a quantitative technique in materials science has increased the requirements for accuracy significantly. Quantifying the thickness or the density of polycrystalline samples with high accuracy using neutron imaging has two main problems: (i) the scattering from the sample creates artefacts on the image and (ii) there is a lack of specific reference attenuation coefficients. This work presents experimental and simulation results to explain and approach these problems. Firstly, a series of neutron radiography and tomography experiments of iron, copper and vanadium are performed and serve as a reference. These materials were selected because they attenuate neutrons mainly through coherent (Fe and Cu) and incoherent (V) scattering. Secondly, an ad hoc Monte Carlo model was developed, based on beamline, sample and detector parameters, in order to simulate experiments, understand the physics involved and interpret the experimental data. The model, developed in the McStas framework, uses a priori information about the sample geometry and crystalline structure, as well as beamline settings, such as spectrum, geometry and detector type. The validity of the simulations is then verified with experimental results for the two problems that motivated this work: (i) the scattering distribution in transmission imaging and (ii) the calculated attenuation coefficients.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Raventós, M.Lehmann, E.H.Boin, M.Morgano, M.Hovind, J.Harti, R.Valsecchi, J.Kaestner, A.Carminati, C.Boillat, P.Trtik, P.Schmid, F.Siegwart, M.Mannes, D.Strobl, M.Grünzweig, C.2018-03-01doi:10.1107/S1600576718001607International Union of CrystallographyThis article describes the development and application of a Monte Carlo tool to improve the quantification capabilities of neutron imaging applied to polycrystals. The combination of modelling and experimentation gives a better understanding of how scattering coming from polycrystalline samples affects neutron imaging experiments.enNEUTRON IMAGING; QUANTIFICATION; NEUTRON SCATTERING; MONTE CARLO METHODSThe development of neutron imaging from a qualitative inspection tool towards a quantitative technique in materials science has increased the requirements for accuracy significantly. Quantifying the thickness or the density of polycrystalline samples with high accuracy using neutron imaging has two main problems: (i) the scattering from the sample creates artefacts on the image and (ii) there is a lack of specific reference attenuation coefficients. This work presents experimental and simulation results to explain and approach these problems. Firstly, a series of neutron radiography and tomography experiments of iron, copper and vanadium are performed and serve as a reference. These materials were selected because they attenuate neutrons mainly through coherent (Fe and Cu) and incoherent (V) scattering. Secondly, an ad hoc Monte Carlo model was developed, based on beamline, sample and detector parameters, in order to simulate experiments, understand the physics involved and interpret the experimental data. The model, developed in the McStas framework, uses a priori information about the sample geometry and crystalline structure, as well as beamline settings, such as spectrum, geometry and detector type. The validity of the simulations is then verified with experimental results for the two problems that motivated this work: (i) the scattering distribution in transmission imaging and (ii) the calculated attenuation coefficients.text/htmlA Monte Carlo approach for scattering correction towards quantitative neutron imaging of polycrystalstext2512018-03-01Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers386med@iucr.orgApril 20183941600-5767Dynamic diffraction artefacts in Bragg coherent diffractive imaging
http://scripts.iucr.org/cgi-bin/paper?te5023
This article reports a theoretical study on the reconstruction artefacts in Bragg coherent diffractive imaging caused by dynamical diffraction effects. It is shown that, unlike the absorption and refraction effects that can be corrected after reconstruction, dynamical diffraction effects have profound impacts on both the amplitude and the phase of the reconstructed complex object, causing strong artefacts. At the dynamical diffraction limit, the reconstructed shape is no longer correct, as a result of the strong extinction effect. Simulations for hemispherical particles of different sizes show the type, magnitude and extent of the dynamical diffraction artefacts, as well as the conditions under which they are negligible.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hu, W.Huang, X.Yan, H.2018-02-01doi:10.1107/S1600576718000274International Union of CrystallographyThe article presents a theoretical study on dynamic artefacts in the reconstruction of Bragg coherent diffractive imaging using an iterative phase retrieval algorithm.enDYNAMIC DIFFRACTION; BRAGG COHERENT DIFFRACTIVE IMAGING; ITERATIVE PHASE RECONSTRUCTIONThis article reports a theoretical study on the reconstruction artefacts in Bragg coherent diffractive imaging caused by dynamical diffraction effects. It is shown that, unlike the absorption and refraction effects that can be corrected after reconstruction, dynamical diffraction effects have profound impacts on both the amplitude and the phase of the reconstructed complex object, causing strong artefacts. At the dynamical diffraction limit, the reconstructed shape is no longer correct, as a result of the strong extinction effect. Simulations for hemispherical particles of different sizes show the type, magnitude and extent of the dynamical diffraction artefacts, as well as the conditions under which they are negligible.text/htmlDynamic diffraction artefacts in Bragg coherent diffractive imagingtext1512018-02-01Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers167med@iucr.orgFebruary 20181741600-5767Interpretation of solution scattering data from lipid nanodiscs
http://scripts.iucr.org/cgi-bin/paper?vg5078
The structural information contained in solution scattering data from empty lipid nanodiscs is examined in the context of a multi-component geometric model. X-ray scattering data were collected on nanodiscs of different compositions at scattering vector magnitudes up to 2.0 Å−1. Through the calculation of the partial form factor for each of the nanodisc components before the isotropic average, structural parameters in the model were correlated to the features observed in the X-ray scattering data and to the corresponding distance distribution function. It is shown that, in general, the features at ∼0.3–0.6 Å−1 in the scattering data correlate to the bilayer structure. The data also support the argument that the elliptical shape of nanodiscs found in model fitting is physical, rather than an artefact due to the nanodisc size distribution. The lipid chain packing peak at ∼1.5 Å−1 is visible in the data and reflects the lipid bilayer phase transition. The shape change in the distance distribution function across the phase transition suggests that the nanodiscs are more circular in the fluid phase. The implication of these findings for model fitting of empty and protein-loaded nanodiscs is discussed.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Graziano, V.Miller, L.Yang, L.2018-02-01doi:10.1107/S1600576717018441International Union of CrystallographySolution scattering data from lipid nanodiscs are interpreted on the basis of X-ray scattering data in an extended range of scattering vectors.enLIPID NANODISCS; SOLUTION SCATTERING; SMALL-ANGLE X-RAY SCATTERING; WIDE-ANGLE X-RAY SCATTERING; SAXS/WAXS; MODELLINGThe structural information contained in solution scattering data from empty lipid nanodiscs is examined in the context of a multi-component geometric model. X-ray scattering data were collected on nanodiscs of different compositions at scattering vector magnitudes up to 2.0 Å−1. Through the calculation of the partial form factor for each of the nanodisc components before the isotropic average, structural parameters in the model were correlated to the features observed in the X-ray scattering data and to the corresponding distance distribution function. It is shown that, in general, the features at ∼0.3–0.6 Å−1 in the scattering data correlate to the bilayer structure. The data also support the argument that the elliptical shape of nanodiscs found in model fitting is physical, rather than an artefact due to the nanodisc size distribution. The lipid chain packing peak at ∼1.5 Å−1 is visible in the data and reflects the lipid bilayer phase transition. The shape change in the distance distribution function across the phase transition suggests that the nanodiscs are more circular in the fluid phase. The implication of these findings for model fitting of empty and protein-loaded nanodiscs is discussed.text/htmlInterpretation of solution scattering data from lipid nanodiscstext1512018-02-01Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers157med@iucr.orgFebruary 20181661600-5767Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals
http://scripts.iucr.org/cgi-bin/paper?te5021
High-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Awel, S.Kirian, R.A.Wiedorn, M.O.Beyerlein, K.R.Roth, N.Horke, D.A.Oberthür, D.Knoska, J.Mariani, V.Morgan, A.Adriano, L.Tolstikova, A.Xavier, P.L.Yefanov, O.Aquila, A.Barty, A.Roy-Chowdhury, S.Hunter, M.S.James, D.Robinson, J.S.Weierstall, U.Rode, A.V.Bajt, S.Küpper, J.Chapman, H.N.2018-02-01doi:10.1107/S1600576717018131International Union of CrystallographyA new particle-injection approach is demonstrated that achieves very low background in the measurement of diffraction from macromolecular nanocrystals by using an aerosol-focusing injector with an X-ray free-electron laser.enX-RAY DIFFRACTION; AEROSOLS; NANOCRYSTALSHigh-resolution Bragg diffraction from aerosolized single granulovirus nanocrystals using an X-ray free-electron laser is demonstrated. The outer dimensions of the in-vacuum aerosol injector components are identical to conventional liquid-microjet nozzles used in serial diffraction experiments, which allows the injector to be utilized with standard mountings. As compared with liquid-jet injection, the X-ray scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. Such reduction is required for diffraction measurements of small macromolecular nanocrystals and single particles. High particle speeds are achieved, making the approach suitable for use at upcoming high-repetition-rate facilities.text/htmlFemtosecond X-ray diffraction from an aerosolized beam of protein nanocrystalstext1512018-02-01Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers133med@iucr.orgFebruary 20181391600-5767Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?yr9017
A figure in the article by Lan, Wierman, Tate, Philipp, Elser & Gruner [J. Appl. Cryst. (2017), 50, 985–993] is corrected.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Lan, T.-Y.Wierman, J.L.Tate, M.W.Philipp, H.T.Elser, V.Gruner, S.M.2018-02-01doi:10.1107/S1600576718000171International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2017), 50, 985–993.enX-RAY SERIAL MICROCRYSTALLOGRAPHY; SPARSE DATA; EMC ALGORITHM; PROTEIN MICROCRYSTALLOGRAPHY; SYNCHROTRON RADIATION SOURCESA figure in the article by Lan, Wierman, Tate, Philipp, Elser & Gruner [J. Appl. Cryst. (2017), 50, 985–993] is corrected.text/htmlReconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns. Corrigendumtext1512018-02-01Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767addenda and errata230med@iucr.orgFebruary 20182301600-5767CAPOW: a standalone program for the calculation of optimal weighting parameters for least-squares crystallographic refinements
http://scripts.iucr.org/cgi-bin/paper?fs5153
The rigorous analysis of crystallographic models, refined through the use of least-squares minimization, is founded on the expectation that the data provided have a normal distribution of residuals. Processed single-crystal diffraction data rarely exhibit this feature without a weighting scheme being applied. These schemes are designed to reflect the precision and accuracy of the measurement of observed reflection intensities. While many programs have the ability to calculate optimal parameters for applied weighting schemes, there are still programs that do not contain this functionality, particularly when moving beyond the spherical atom model. For this purpose, CAPOW (calculation and plotting of optimal weights), a new program for the calculation of optimal weighting parameters for a SHELXL weighting scheme, is presented and an example of its application in a multipole refinement is given.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Johnson, N.T.Ott, H.Probert, M.R.2018-02-01doi:10.1107/S1600576717016600International Union of CrystallographyA new standalone program to calculate optimized values for weighting parameters, CAPOW, is presented along with enhanced visualization tools for analysing statistical distributions of data.enCHARGE DENSITY; MULTIPOLAR REFINEMENT; WEIGHTINGThe rigorous analysis of crystallographic models, refined through the use of least-squares minimization, is founded on the expectation that the data provided have a normal distribution of residuals. Processed single-crystal diffraction data rarely exhibit this feature without a weighting scheme being applied. These schemes are designed to reflect the precision and accuracy of the measurement of observed reflection intensities. While many programs have the ability to calculate optimal parameters for applied weighting schemes, there are still programs that do not contain this functionality, particularly when moving beyond the spherical atom model. For this purpose, CAPOW (calculation and plotting of optimal weights), a new program for the calculation of optimal weighting parameters for a SHELXL weighting scheme, is presented and an example of its application in a multipole refinement is given.text/htmlCAPOW: a standalone program for the calculation of optimal weighting parameters for least-squares crystallographic refinementstext1512018-02-01Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs200med@iucr.orgFebruary 20182041600-57673DBVSMAPPER: a program for automatically generating bond-valence sum landscapes. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?to9016
An equation in the article by Sale & Avdeev [J. Appl. Cryst. (2012), 45, 1054–1056] is corrected.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Sale, M.Avdeev, M.2017-11-14doi:10.1107/S1600576717016119International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2012), 45, 1054–1056.enBOND-VALENCE SUMS; BOND-VALENCE SUM MAPPING; BOND-VALENCE ENERGY LANDSCAPE; ISOSURFACES; AUTOMATION; ION-CONDUCTION PATHWAYS; TOPOLOGY; CIF; PERL; MATERIALS STUDIOAn equation in the article by Sale & Avdeev [J. Appl. Cryst. (2012), 45, 1054–1056] is corrected.text/html3DBVSMAPPER: a program for automatically generating bond-valence sum landscapes. Corrigendumtext6502017-11-14Journal of Applied CrystallographyCopyright (c) 2017 International Union of Crystallography1600-5767addenda and errata1852med@iucr.orgDecember 201718521600-5767Hierarchical clustering for multiple-crystal macromolecular crystallography experiments: the ccCluster program
http://scripts.iucr.org/cgi-bin/paper?ap5019
This article describes ccCluster, a software providing an intuitive graphical user interface (GUI) and multiple functions to perform hierarchical cluster analysis on multiple crystallographic datasets. The program makes it easier for users to choose, in the case of multi-crystal data collection, those datasets that will be merged together to give good final statistics. It provides a simple GUI to analyse the dendrogram and various options for automated clustering and data merging.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Santoni, G.Zander, U.Mueller-Dieckmann, C.Leonard, G.Popov, A.2017-11-29doi:10.1107/S1600576717015229International Union of CrystallographyThe ccCluster program provides an easy-to-use interface to perform hierarchical cluster analysis on protein diffraction datasets.enCLUSTER ANALYSIS; SERIAL CRYSTALLOGRAPHY; MULTICRYSTAL DATA COLLECTION; PHASINGThis article describes ccCluster, a software providing an intuitive graphical user interface (GUI) and multiple functions to perform hierarchical cluster analysis on multiple crystallographic datasets. The program makes it easier for users to choose, in the case of multi-crystal data collection, those datasets that will be merged together to give good final statistics. It provides a simple GUI to analyse the dendrogram and various options for automated clustering and data merging.text/htmlHierarchical clustering for multiple-crystal macromolecular crystallography experiments: the ccCluster programtext6502017-11-29Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1844med@iucr.orgDecember 201718511600-5767The modular small-angle X-ray scattering data correction sequence
http://scripts.iucr.org/cgi-bin/paper?vg5075
Data correction is probably the least favourite activity amongst users experimenting with small-angle X-ray scattering: if it is not done sufficiently well, this may become evident only during the data analysis stage, necessitating the repetition of the data corrections from scratch. A recommended comprehensive sequence of elementary data correction steps is presented here to alleviate the difficulties associated with data correction, both in the laboratory and at the synchrotron. When applied in the proposed order to the raw signals, the resulting absolute scattering cross section will provide a high degree of accuracy for a very wide range of samples, with its values accompanied by uncertainty estimates. The method can be applied without modification to any pinhole-collimated instruments with photon-counting direct-detection area detectors.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Pauw, B.R.Smith, A.J.Snow, T.Terrill, N.J.Thünemann, A.F.2017-11-29doi:10.1107/S1600576717015096International Union of CrystallographyA data correction sequence is presented, consisting of ordered elementary steps that extract the small-angle X-ray scattering cross section from the original detector signal(s). It is applicable to a wide range of samples, including solids and dispersions.enSMALL-ANGLE SCATTERING; ACCURACY; METHODOLOGY; DATA CORRECTIONData correction is probably the least favourite activity amongst users experimenting with small-angle X-ray scattering: if it is not done sufficiently well, this may become evident only during the data analysis stage, necessitating the repetition of the data corrections from scratch. A recommended comprehensive sequence of elementary data correction steps is presented here to alleviate the difficulties associated with data correction, both in the laboratory and at the synchrotron. When applied in the proposed order to the raw signals, the resulting absolute scattering cross section will provide a high degree of accuracy for a very wide range of samples, with its values accompanied by uncertainty estimates. The method can be applied without modification to any pinhole-collimated instruments with photon-counting direct-detection area detectors.text/htmlThe modular small-angle X-ray scattering data correction sequencetext6502017-11-29Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1800med@iucr.orgDecember 201718111600-5767Variant selection in surface martensite
http://scripts.iucr.org/cgi-bin/paper?nb5203
A significant variant selection is reported in isothermal martensite formed on the surface of an Fe–30% Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic–body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}γ habit plane and the accommodation mechanism by twin-related variant pairing.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Baur, A.P.Cayron, C.Logé, R.E.2017-10-20doi:10.1107/S160057671701398XInternational Union of CrystallographyVariant selection is reported in martensite formed on the surface of an Fe–30% Ni sample. Predictive models of the phenomenon based on different crystallographic descriptions of the transformation are proposed and compared.enSURFACE MARTENSITE; VARIANT SELECTION; PHENOMENOLOGICAL THEORY OF MARTENSITE CRYSTALLOGRAPHY (PTMC); CONTINUOUS F.C.C.-B.C.C. DISTORTIONA significant variant selection is reported in isothermal martensite formed on the surface of an Fe–30% Ni sample. The selection phenomenon is modelled using different descriptions of the martensitic phase transformation. In particular, matrices based on the phenomenological theory of martensite crystallography, the Jaswon and Wheeler distortion, and the continuous face centred cubic–body centred cubic distortion are compared. All descriptions allow good predictions of the variant selection. However, the Jaswon and Wheeler distortion and the continuous distortion better account for other features of the surface martensite, such as the {225}γ habit plane and the accommodation mechanism by twin-related variant pairing.text/htmlVariant selection in surface martensitetext6502017-10-20Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1646med@iucr.orgDecember 201716521600-5767The electrostatic potential of dynamic charge densities
http://scripts.iucr.org/cgi-bin/paper?ks5578
A procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of dl-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at T = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å−3 isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hübschle, C.B.van Smaalen, S.2017-10-20doi:10.1107/S1600576717013802International Union of CrystallographyThe electrostatic potential (ESP) is computed for dynamic charge densities corresponding to multipole models and maximum-entropy densities. Convergence of the reciprocal-space summation is guaranteed by the Gaussian form of the Debye–Waller factor. Applications to serine demonstrate only a weak temperature dependence of the ESP on molecular surfaces relevant to intermolecular interactions.enELECTROSTATIC POTENTIAL; CHARGE DENSITY; ELECTRON DENSITY; X-RAY DIFFRACTION; MULTIPOLE MODELA procedure to derive the electrostatic potential (ESP) for dynamic charge densities obtained from structure models or maximum-entropy densities is introduced. The ESP essentially is obtained by inverse Fourier transform of the dynamic structure factors of the total charge density corresponding to the independent atom model, the multipole model or maximum-entropy densities, employing dedicated software that will be part of the BayMEM software package. Our approach is also discussed with respect to the Ewald summation method. It is argued that a meaningful ESP can only be obtained if identical thermal smearing is applied to the nuclear (positive) and electronic (negative) parts of the dynamic charge densities. The method is applied to structure models of dl-serine at three different temperatures of 20, 100 and 298 K. The ESP at locations near the atomic nuclei exhibits a drastic reduction with increasing temperature, the largest difference between the ESP from the static charge density and the ESP of the dynamic charge density being at T = 20 K. These features demonstrate that zero-point vibrations are sufficient for changing the spiky nature of the ESP at the nuclei into finite values. On 0.5 e Å−3 isosurfaces of the electron densities (taken as the molecular surface relevant to intermolecular interactions), the dynamic ESP is surprisingly similar at all temperatures, while the static ESP of a single molecule has a slightly larger range and is shifted towards positive potential values.text/htmlThe electrostatic potential of dynamic charge densitiestext6502017-10-20Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1627med@iucr.orgDecember 201716361600-5767Bayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurements
http://scripts.iucr.org/cgi-bin/paper?rg5136
Monte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3 film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Anada, M.Nakanishi-Ohno, Y.Okada, M.Kimura, T.Wakabayashi, Y.2017-10-20doi:10.1107/S1600576717013292International Union of CrystallographyReverse Monte Carlo software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference.enBAYESIAN INFERENCE; CRYSTAL TRUNCATION RODS; PEROVSKITE FILMS; MONTE CARLOMonte Carlo (MC)-based refinement software to analyze the atomic arrangements of perovskite oxide ultrathin films from the crystal truncation rod intensity is developed on the basis of Bayesian inference. The advantages of the MC approach are (i) it is applicable to multi-domain structures, (ii) it provides the posterior probability of structures through Bayes' theorem, which allows one to evaluate the uncertainty of estimated structural parameters, and (iii) one can involve any information provided by other experiments and theories. The simulated annealing procedure efficiently searches for the optimum model owing to its stochastic updates, regardless of the initial values, without being trapped by local optima. The performance of the software is examined with a five-unit-cell-thick LaAlO3 film fabricated on top of SrTiO3. The software successfully found the global optima from an initial model prepared by a small grid search calculation. The standard deviations of the atomic positions derived from a dataset taken at a second-generation synchrotron are ±0.02 Å for metal sites and ±0.03 Å for oxygen sites.text/htmlBayesian inference of metal oxide ultrathin film structure based on crystal truncation rod measurementstext6502017-10-20Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1611med@iucr.orgDecember 201716161600-5767Expanding Lorentz and spectrum corrections to large volumes of reciprocal space for single-crystal time-of-flight neutron diffraction. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?fs9119
The author list of the article by Michels-Clark et al. [J. Appl. Cryst. (2016), 49, 497–506] is amended with the addition of Michal Chodkiewicz, Thomas Weber and Hans-Beat Bürgi. The complete list of authors is Tara Michels-Clark, Andrei Savici, Vickie Lynch, Xiaoping Wang, Michal Chodkiewicz, Thomas Weber, Hans-Beat Bürgi and Christina Hoffmann.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Michels-Clark, T.M.Savici, A.T.Lynch, V.E.Wang, X.Chodkiewicz, M.Weber, T.Bürgi, H.-B.Hoffmann, C.M.2017-09-25doi:10.1107/S1600576717006781International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2016), 49, 497–506: addition of co-authors.enMODULATED DIFFUSE SCATTERING; LOCAL STRUCTURE MODELING; LORENTZ AND SPECTRUM CORRECTIONS; SINGLE-CRYSTAL TIME-OF-FLIGHT NEUTRON DIFFRACTIONThe author list of the article by Michels-Clark et al. [J. Appl. Cryst. (2016), 49, 497–506] is amended with the addition of Michal Chodkiewicz, Thomas Weber and Hans-Beat Bürgi. The complete list of authors is Tara Michels-Clark, Andrei Savici, Vickie Lynch, Xiaoping Wang, Michal Chodkiewicz, Thomas Weber, Hans-Beat Bürgi and Christina Hoffmann.text/htmlExpanding Lorentz and spectrum corrections to large volumes of reciprocal space for single-crystal time-of-flight neutron diffraction. Corrigendumtext5502017-09-25Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767addenda and errata1559med@iucr.orgOctober 201715591600-5767Nanocrystallography measurements of early stage synthetic malaria pigment
http://scripts.iucr.org/cgi-bin/paper?ap5010
The recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data. If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Dilanian, R.A.Streltsov, V.Coughlan, H.D.Quiney, H.M.Martin, A.V.Klonis, N.Dogovski, C.Boutet, S.Messerschmidt, M.Williams, G.J.Williams, S.Phillips, N.W.Nugent, K.A.Tilley, L.Abbey, B.2017-09-28doi:10.1107/S1600576717012663International Union of CrystallographySerial femtosecond crystallography (SFX) at an X-ray free-electron laser enables crystllographic data to be collected from samples orders of magnitude smaller than at a synchrotron. Here SFX is used to investigate the nascent structure of β-hematin derived from nanocrystals and this is compared with the well known structure derived from macroscopic crystals of the same material.enCRYSTALLOGRAPHY; SERIAL FEMTOSECOND NANOCRYSTALLOGRAPHY; MALARIA; CRYSTALLINE DISORDER; STRUCTURAL INHOMOGENIETYThe recent availability of extremely intense, femtosecond X-ray free-electron laser (XFEL) sources has spurred the development of serial femtosecond nanocrystallography (SFX). Here, SFX is used to analyze nanoscale crystals of β-hematin, the synthetic form of hemozoin which is a waste by-product of the malaria parasite. This analysis reveals significant differences in β-hematin data collected during SFX and synchrotron crystallography experiments. To interpret these differences two possibilities are considered: structural differences between the nanocrystal and larger crystalline forms of β-hematin, and radiation damage. Simulation studies show that structural inhomogeneity appears at present to provide a better fit to the experimental data. If confirmed, these observations will have implications for designing compounds that inhibit hemozoin formation and suggest that, for some systems at least, additional information may be gained by comparing structures obtained from nanocrystals and macroscopic crystals of the same molecule.text/htmlNanocrystallography measurements of early stage synthetic malaria pigmenttext5502017-09-28Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1533med@iucr.orgOctober 201715401600-5767Quantifying adsorption-induced deformation of nanoporous materials on different length scales
http://scripts.iucr.org/cgi-bin/paper?vg5076
A new in situ setup combining small-angle neutron scattering (SANS) and dilatometry was used to measure water-adsorption-induced deformation of a monolithic silica sample with hierarchical porosity. The sample exhibits a disordered framework consisting of macropores and struts containing two-dimensional hexagonally ordered cylindrical mesopores. The use of an H2O/D2O water mixture with zero scattering length density as an adsorptive allows a quantitative determination of the pore lattice strain from the shift of the corresponding diffraction peak. This radial strut deformation is compared with the simultaneously measured macroscopic length change of the sample with dilatometry, and differences between the two quantities are discussed on the basis of the deformation mechanisms effective at the different length scales. It is demonstrated that the SANS data also provide a facile way to quantitatively determine the adsorption isotherm of the material by evaluating the incoherent scattering contribution of H2O at large scattering vectors.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Morak, R.Braxmeier, S.Ludescher, L.Putz, F.Busch, S.Hüsing, N.Reichenauer, G.Paris, O.2017-09-14doi:10.1107/S1600576717012274International Union of CrystallographySimultaneous small-angle neutron scattering and dilatometry reveal water-adsorption-induced deformation of silica materials with hierarchical porosity along with their adsorption isotherm.enMESOPOROUS MATERIALS; SMALL-ANGLE NEUTRON SCATTERING; DILATOMETRY; ADSORPTION-INDUCED DEFORMATION; ADSORPTION ISOTHERMSA new in situ setup combining small-angle neutron scattering (SANS) and dilatometry was used to measure water-adsorption-induced deformation of a monolithic silica sample with hierarchical porosity. The sample exhibits a disordered framework consisting of macropores and struts containing two-dimensional hexagonally ordered cylindrical mesopores. The use of an H2O/D2O water mixture with zero scattering length density as an adsorptive allows a quantitative determination of the pore lattice strain from the shift of the corresponding diffraction peak. This radial strut deformation is compared with the simultaneously measured macroscopic length change of the sample with dilatometry, and differences between the two quantities are discussed on the basis of the deformation mechanisms effective at the different length scales. It is demonstrated that the SANS data also provide a facile way to quantitatively determine the adsorption isotherm of the material by evaluating the incoherent scattering contribution of H2O at large scattering vectors.text/htmlQuantifying adsorption-induced deformation of nanoporous materials on different length scalestext5502017-09-14Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1404med@iucr.orgOctober 201714101600-5767Calibrating SANS data for instrument geometry and pixel sensitivity effects: access to an extended Q range
http://scripts.iucr.org/cgi-bin/paper?ks5569
An improved data-reduction procedure is proposed and demonstrated for small-angle neutron scattering (SANS) measurements. Its main feature is the correction of geometry- and wavelength-dependent intensity variations on the detector in a separate step from the different pixel sensitivities: the geometric and wavelength effects can be corrected analytically, while pixel sensitivities have to be calibrated to a reference measurement. The geometric effects are treated for position-sensitive 3He proportional counter tubes, where they are anisotropic owing to the cylindrical geometry of the gas tubes. For the calibration of pixel sensitivities, a procedure is developed that is valid for isotropic and anisotropic signals. The proposed procedure can save a significant amount of beamtime which has hitherto been used for calibration measurements.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Karge, L.Gilles, R.Busch, S.2017-09-14doi:10.1107/S1600576717011463International Union of CrystallographyA calibration procedure for small-angle neutron scattering (SANS) data is presented, where geometric effects are treated analytically and voxel sensitivities are calibrated with measurements of an arbitrary scatterer. This allows correction of the measured intensities with a single measurement, without the need to measure an isotropic scatterer at all used instrumental settings.enSMALL-ANGLE NEUTRON SCATTERING; DATA REDUCTION; CALIBRATION; CORRECTIONSAn improved data-reduction procedure is proposed and demonstrated for small-angle neutron scattering (SANS) measurements. Its main feature is the correction of geometry- and wavelength-dependent intensity variations on the detector in a separate step from the different pixel sensitivities: the geometric and wavelength effects can be corrected analytically, while pixel sensitivities have to be calibrated to a reference measurement. The geometric effects are treated for position-sensitive 3He proportional counter tubes, where they are anisotropic owing to the cylindrical geometry of the gas tubes. For the calibration of pixel sensitivities, a procedure is developed that is valid for isotropic and anisotropic signals. The proposed procedure can save a significant amount of beamtime which has hitherto been used for calibration measurements.text/htmlCalibrating SANS data for instrument geometry and pixel sensitivity effects: access to an extended Q rangetext5502017-09-14Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1382med@iucr.orgOctober 201713941600-5767BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis
http://scripts.iucr.org/cgi-bin/paper?ge5036
BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size-exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed-source programs such as Primus and ScÅtter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hopkins, J.B.Gillilan, R.E.Skou, S.2017-09-05doi:10.1107/S1600576717011438International Union of CrystallographyBioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data, including size-exclusion chromatography coupled SAXS data. The software is designed for biological data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and more advanced analyses such as calculation of inverse Fourier transforms.enSMALL-ANGLE X-RAY SCATTERING; SAXS; DATA ANALYSIS; SIZE EXCLUSION CHROMATOGRAPHY; SEC-SAXS; COMPUTER PROGRAMS; BIOXTAS RAWBioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size-exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed-source programs such as Primus and ScÅtter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.text/htmlBioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysistext5502017-09-05Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1545med@iucr.orgOctober 201715531600-5767Berkeley Screen: a set of 96 solutions for general macromolecular crystallization
http://scripts.iucr.org/cgi-bin/paper?ei5025
Using statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Pereira, J.H.McAndrew, R.P.Tomaleri, G.P.Adams, P.D.2017-09-05doi:10.1107/S1600576717011347International Union of CrystallographyThe Berkeley Screen provides an efficient set of solutions for general macromolecular crystallization trials.enCRYSTALLIZATION SCREENS; CRYSTAL PACKING; IONS AND BUFFERS; CRYSTAL GROWTH; STRUCTURAL BIOLOGYUsing statistical analysis of the Biological Macromolecular Crystallization Database, combined with previous knowledge about crystallization reagents, a crystallization screen called the Berkeley Screen has been created. Correlating crystallization conditions and high-resolution protein structures, it is possible to better understand the influence that a particular solution has on protein crystal formation. Ions and small molecules such as buffers and precipitants used in crystallization experiments were identified in electron density maps, highlighting the role of these chemicals in protein crystal packing. The Berkeley Screen has been extensively used to crystallize target proteins from the Joint BioEnergy Institute and the Collaborative Crystallography program at the Berkeley Center for Structural Biology, contributing to several Protein Data Bank entries and related publications. The Berkeley Screen provides the crystallographic community with an efficient set of solutions for general macromolecular crystallization trials, offering a valuable alternative to the existing commercially available screens.text/htmlBerkeley Screen: a set of 96 solutions for general macromolecular crystallizationtext5502017-09-05Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1352med@iucr.orgOctober 201713581600-5767Direction indices for crystal lattices
http://scripts.iucr.org/cgi-bin/paper?gj5187
Direction indices [uvw] of rational directions in crystal lattices are commonly restricted to integer numbers. This restriction is correct only when primitive unit cells are used. In the case of centred cells, however, direction indices may take fractional values too, because the first lattice node after the origin along a direction can have fractional coordinates in a centred basis. This evidence is very often overlooked and an undue simplification of direction indices to integer values is usually adopted. Although such a simplification does not affect the identification of the direction, it is potentially a source of confusion and mistakes in crystallographic calculations. A parallel is made with the incorrect restriction of Miller indices to relatively prime integers in centred cells.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Nespolo, M.2017-08-09doi:10.1107/S1600576717010548International Union of CrystallographyThe incorrect restriction to integer values for direction indices in centred cells and the potential consequences are pointed out and corrected.enDIRECTION INDICES; MILLER INDICES; CENTRED CELLSDirection indices [uvw] of rational directions in crystal lattices are commonly restricted to integer numbers. This restriction is correct only when primitive unit cells are used. In the case of centred cells, however, direction indices may take fractional values too, because the first lattice node after the origin along a direction can have fractional coordinates in a centred basis. This evidence is very often overlooked and an undue simplification of direction indices to integer values is usually adopted. Although such a simplification does not affect the identification of the direction, it is potentially a source of confusion and mistakes in crystallographic calculations. A parallel is made with the incorrect restriction of Miller indices to relatively prime integers in centred cells.text/htmlDirection indices for crystal latticestext5502017-08-09Journal of Applied CrystallographyCopyright (c) 2017 International Union of Crystallography1600-5767teaching and education1541med@iucr.orgOctober 201715441600-5767Nanoparticle size distribution quantification: results of a small-angle X-ray scattering inter-laboratory comparison
http://scripts.iucr.org/cgi-bin/paper?ge5041
This paper presents the first worldwide inter-laboratory comparison of small-angle X-ray scattering (SAXS) for nanoparticle sizing. The measurands in this comparison are the mean particle radius, the width of the size distribution and the particle concentration. The investigated sample consists of dispersed silver nanoparticles, surrounded by a stabilizing polymeric shell of poly(acrylic acid). The silver cores dominate the X-ray scattering pattern, leading to the determination of their radius size distribution using (i) the generalized indirect Fourier transformation method, (ii) classical model fitting using SASfit and (iii) a Monte Carlo fitting approach using McSAS. The application of these three methods to the collected data sets from the various laboratories produces consistent mean number- and volume-weighted core radii of Rn = 2.76 (6) nm and Rv = 3.20 (4) nm, respectively. The corresponding widths of the lognormal radius distribution of the particles were σn = 0.65 (1) nm and σv = 0.71 (1) nm. The particle concentration determined using this method was 3.0 (4) g l−1 or 4.2 (7) × 10−6 mol l−1. These results are affected slightly by the choice of data evaluation procedure, but not by the instruments: the participating laboratories at synchrotron SAXS beamlines, commercial and in-house-designed instruments were all able to provide highly consistent data. This demonstrates that SAXS is a suitable method for revealing particle size distributions in the sub-20 nm region (at minimum), out of reach for most other analytical methods.https://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Pauw, B.R.Kästner, C.Thünemann, A.F.2017-08-18doi:10.1107/S160057671701010XInternational Union of CrystallographyAn extensive round robin experiment between small-angle X-ray scattering laboratories has delivered a global uncertainty estimate for the measurands of a nanoparticle dispersion. Irrespective of the instrument pedigree, the distribution mean, width and volume fraction could be determined with an accuracy of 1, 10 and 10%, respectively.enSMALL-ANGLE SCATTERING; ACCURACY; METHODOLOGY; SILVER NANOPARTICLES; POLY(ACRYLIC ACID); SASFIT; MCSAS; INVERSE FOURIER TRANSFORM; ROUND ROBINThis paper presents the first worldwide inter-laboratory comparison of small-angle X-ray scattering (SAXS) for nanoparticle sizing. The measurands in this comparison are the mean particle radius, the width of the size distribution and the particle concentration. The investigated sample consists of dispersed silver nanoparticles, surrounded by a stabilizing polymeric shell of poly(acrylic acid). The silver cores dominate the X-ray scattering pattern, leading to the determination of their radius size distribution using (i) the generalized indirect Fourier transformation method, (ii) classical model fitting using SASfit and (iii) a Monte Carlo fitting approach using McSAS. The application of these three methods to the collected data sets from the various laboratories produces consistent mean number- and volume-weighted core radii of Rn = 2.76 (6) nm and Rv = 3.20 (4) nm, respectively. The corresponding widths of the lognormal radius distribution of the particles were σn = 0.65 (1) nm and σv = 0.71 (1) nm. The particle concentration determined using this method was 3.0 (4) g l−1 or 4.2 (7) × 10−6 mol l−1. These results are affected slightly by the choice of data evaluation procedure, but not by the instruments: the participating laboratories at synchrotron SAXS beamlines, commercial and in-house-designed instruments were all able to provide highly consistent data. This demonstrates that SAXS is a suitable method for revealing particle size distributions in the sub-20 nm region (at minimum), out of reach for most other analytical methods.text/htmlNanoparticle size distribution quantification: results of a small-angle X-ray scattering inter-laboratory comparisontext5502017-08-18Journal of Applied Crystallographyhttps://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1280med@iucr.orgOctober 201712881600-5767Ewald: an extended wide-angle Laue diffractometer for the second target station of the Spallation Neutron Source
http://scripts.iucr.org/cgi-bin/paper?fs5150
Visualizing hydrogen atoms in biological materials is one of the biggest remaining challenges in biophysical analysis. While X-ray techniques have unrivaled capacity for high-throughput structure determination, neutron diffraction is uniquely sensitive to hydrogen atom positions in crystals of biological materials and can provide a more complete picture of the atomic and electronic structures of biological macromolecules. This information can be essential in providing predictive understanding and engineering control of key biological processes, for example, in catalysis, ligand binding and light harvesting, and to guide bioengineering of enzymes and drug design. One very common and large capability gap for all neutron atomic resolution single-crystal diffractometers is the weak flux of available neutron beams, which results in limited signal-to-noise ratios giving a requirement for sample volumes of at least 0.1 mm3. The ability to operate on crystals an order of magnitude smaller (0.01 mm3) will open up new and more complex systems to studies with neutrons which will help in our understanding of enzyme mechanisms and enable us to improve drugs against multi resistant bacteria. With this is mind, an extended wide-angle Laue diffractometer, `Ewald', has been designed, which can collect data using crystal volumes below 0.01 mm3.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Coates, L.Robertson, L.2017-07-26doi:10.1107/S1600576717010032International Union of CrystallographyThe design of a macromolecular neutron diffractometer for the second target station of the Spallation Neutron Source is detailed.enNEUTRON DIFFRACTION; PROTEIN CRYSTALLOGRAPHYVisualizing hydrogen atoms in biological materials is one of the biggest remaining challenges in biophysical analysis. While X-ray techniques have unrivaled capacity for high-throughput structure determination, neutron diffraction is uniquely sensitive to hydrogen atom positions in crystals of biological materials and can provide a more complete picture of the atomic and electronic structures of biological macromolecules. This information can be essential in providing predictive understanding and engineering control of key biological processes, for example, in catalysis, ligand binding and light harvesting, and to guide bioengineering of enzymes and drug design. One very common and large capability gap for all neutron atomic resolution single-crystal diffractometers is the weak flux of available neutron beams, which results in limited signal-to-noise ratios giving a requirement for sample volumes of at least 0.1 mm3. The ability to operate on crystals an order of magnitude smaller (0.01 mm3) will open up new and more complex systems to studies with neutrons which will help in our understanding of enzyme mechanisms and enable us to improve drugs against multi resistant bacteria. With this is mind, an extended wide-angle Laue diffractometer, `Ewald', has been designed, which can collect data using crystal volumes below 0.01 mm3.text/htmlEwald: an extended wide-angle Laue diffractometer for the second target station of the Spallation Neutron Sourcetext4502017-07-26Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1174med@iucr.orgAugust 201711781600-5767SAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissues
http://scripts.iucr.org/cgi-bin/paper?fs5146
This article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions. Finally, the software combines functionality for determination of collagen spatial order parameters with a rudimentary orientation plot capability.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Abass, A.Bell, J.S.Spang, M.T.Hayes, S.Meek, K.M.Boote, C.2017-07-07doi:10.1107/S1600576717007877International Union of CrystallographySAXS4COLL is an interactive computer program for reduction and analysis of small-angle X-ray scattering data from fibrous collagen tissues, combining data reduction, bespoke background subtraction, semi-automated peak detection and calibration.enSMALL-ANGLE X-RAY SCATTERING; FIBRILLAR COLLAGEN; DATA REDUCTION; DATA PROCESSINGThis article provides an overview of a new integrated software tool for reduction and analysis of small-angle X-ray scattering (SAXS) data from fibrous collagen tissues, with some wider applicability to other cylindrically symmetric scattering systems. SAXS4COLL combines interactive features for data pre-processing, bespoke background subtraction, semi-automated peak detection and calibration. Both equatorial and meridional SAXS peak parameters can be measured, and the former can be deconstructed into cylinder and lattice contributions. Finally, the software combines functionality for determination of collagen spatial order parameters with a rudimentary orientation plot capability.text/htmlSAXS4COLL: an integrated software tool for analysing fibrous collagen-based tissuestext4502017-07-07Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1235med@iucr.orgAugust 201712401600-5767ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions
http://scripts.iucr.org/cgi-bin/paper?ge5042
ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data. This article summarizes the progress made during the 2.5–2.8 ATSAS release series and highlights the latest developments. These include AMBIMETER, an assessment of the reconstruction ambiguity of experimental data; DATCLASS, a multiclass shape classification based on experimental data; SASRES, for estimating the resolution of ab initio model reconstructions; CHROMIXS, a convenient interface to analyse in-line size exclusion chromatography data; SHANUM, to evaluate the useful angular range in measured data; SREFLEX, to refine available high-resolution models using normal mode analysis; SUPALM for a rapid superposition of low- and high-resolution models; and SASPy, the ATSAS plugin for interactive modelling in PyMOL. All these features and other improvements are included in the ATSAS release 2.8, freely available for academic users from https://www.embl-hamburg.de/biosaxs/software.html.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Franke, D.Petoukhov, M.V.Konarev, P.V.Panjkovich, A.Tuukkanen, A.Mertens, H.D.T.Kikhney, A.G.Hajizadeh, N.R.Franklin, J.M.Jeffries, C.M.Svergun, D.I.2017-06-26doi:10.1107/S1600576717007786International Union of CrystallographyDevelopments and improvements of the ATSAS software suite (versions 2.5–2.8) for analysis of small-angle scattering data of biological macromolecules or nanoparticles are described.enSMALL-ANGLE SCATTERING; DATA ANALYSIS; BIOLOGICAL MACROMOLECULES; STRUCTURAL MODELLING; ATSASATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data. This article summarizes the progress made during the 2.5–2.8 ATSAS release series and highlights the latest developments. These include AMBIMETER, an assessment of the reconstruction ambiguity of experimental data; DATCLASS, a multiclass shape classification based on experimental data; SASRES, for estimating the resolution of ab initio model reconstructions; CHROMIXS, a convenient interface to analyse in-line size exclusion chromatography data; SHANUM, to evaluate the useful angular range in measured data; SREFLEX, to refine available high-resolution models using normal mode analysis; SUPALM for a rapid superposition of low- and high-resolution models; and SASPy, the ATSAS plugin for interactive modelling in PyMOL. All these features and other improvements are included in the ATSAS release 2.8, freely available for academic users from https://www.embl-hamburg.de/biosaxs/software.html.text/htmlATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutionstext4502017-06-26Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1212med@iucr.orgAugust 201712251600-5767Grazing-incidence small-angle neutron scattering from structures below an interface
http://scripts.iucr.org/cgi-bin/paper?ge5039
Changes of scattering are observed as the grazing angle of incidence of an incoming beam increases and probes different depths in samples. A model has been developed to describe the observed intensity in grazing-incidence small-angle neutron scattering (GISANS) experiments. This includes the significant effects of instrument resolution, the sample transmission, which depends on both absorption and scattering, and the sample structure. The calculations are tested with self-organized structures of two colloidal samples with different size particles that were measured on two different instruments. The model allows calculations for various instruments with defined resolution and can be used to design future improved experiments. The possibilities and limits of GISANS for different studies are discussed using the model calculations.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Nouhi, S.Hellsing, M.S.Kapaklis, V.Rennie, A.R.2017-07-07doi:10.1107/S1600576717007518International Union of CrystallographyCalculations of intensity in grazing-incidence small-angle neutron scattering are made for colloidal structures near a solid/liquid interface.enGRAZING-INCIDENCE SMALL-ANGLE NEUTRON SCATTERING; GISANS; COLLOIDAL PARTICLES; SOLID/LIQUID INTERFACESChanges of scattering are observed as the grazing angle of incidence of an incoming beam increases and probes different depths in samples. A model has been developed to describe the observed intensity in grazing-incidence small-angle neutron scattering (GISANS) experiments. This includes the significant effects of instrument resolution, the sample transmission, which depends on both absorption and scattering, and the sample structure. The calculations are tested with self-organized structures of two colloidal samples with different size particles that were measured on two different instruments. The model allows calculations for various instruments with defined resolution and can be used to design future improved experiments. The possibilities and limits of GISANS for different studies are discussed using the model calculations.text/htmlGrazing-incidence small-angle neutron scattering from structures below an interfacetext4502017-07-07Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1066med@iucr.orgAugust 201710741600-5767Continuous diffraction of molecules and disordered molecular crystals
http://scripts.iucr.org/cgi-bin/paper?jo5031
The intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities. This situation arises in the continuous diffraction of laser-aligned molecules or translationally disordered molecular crystals. This paper develops the analysis of the intensity statistics of such continuous diffraction to obtain parameters such as scaling, beam coherence and the number of contributing independent object orientations. When measured, continuous molecular diffraction is generally weak and accompanied by a background that far exceeds the strength of the signal. Instead of just relying upon the smallest measured intensities or their mean value to guide the subtraction of the background, it is shown how all measured values can be utilized to estimate the background, noise and signal, by employing a modified `noisy Wilson' distribution that explicitly includes the background. Parameters relating to the background and signal quantities can be estimated from the moments of the measured intensities. The analysis method is demonstrated on previously published continuous diffraction data measured from crystals of photosystem II [Ayyer et al. (2016), Nature, 530, 202–206].http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Chapman, H.N.Yefanov, O.M.Ayyer, K.White, T.A.Barty, A.Morgan, A.Mariani, V.Oberthuer, D.Pande, K.2017-07-07doi:10.1107/S160057671700749XInternational Union of CrystallographyThe statistics of continuous diffraction patterns are determined and used to improve analysis of the diffraction of imperfect crystals of photosystem II.enCONTINUOUS DIFFRACTION; DISORDERED CRYSTALS; STATISTICS; PHOTOSYSTEM II; DIFFUSE SCATTERINGThe intensities of far-field diffraction patterns of orientationally aligned molecules obey Wilson statistics, whether those molecules are in isolation (giving rise to a continuous diffraction pattern) or arranged in a crystal (giving rise to Bragg peaks). Ensembles of molecules in several orientations, but uncorrelated in position, give rise to the incoherent sum of the diffraction from those objects, modifying the statistics in a similar way as crystal twinning modifies the distribution of Bragg intensities. This situation arises in the continuous diffraction of laser-aligned molecules or translationally disordered molecular crystals. This paper develops the analysis of the intensity statistics of such continuous diffraction to obtain parameters such as scaling, beam coherence and the number of contributing independent object orientations. When measured, continuous molecular diffraction is generally weak and accompanied by a background that far exceeds the strength of the signal. Instead of just relying upon the smallest measured intensities or their mean value to guide the subtraction of the background, it is shown how all measured values can be utilized to estimate the background, noise and signal, by employing a modified `noisy Wilson' distribution that explicitly includes the background. Parameters relating to the background and signal quantities can be estimated from the moments of the measured intensities. The analysis method is demonstrated on previously published continuous diffraction data measured from crystals of photosystem II [Ayyer et al. (2016), Nature, 530, 202–206].text/htmlContinuous diffraction of molecules and disordered molecular crystalstext4502017-07-07Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1084med@iucr.orgAugust 201711031600-5767FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images
http://scripts.iucr.org/cgi-bin/paper?te5022
A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues–Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on (\overline 110) facets.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Beyerlein, K.R.White, T.A.Yefanov, O.Gati, C.Kazantsev, I.G.Nielsen, N.F.-G.Larsen, P.M.Chapman, H.N.Schmidt, S.2017-07-07doi:10.1107/S1600576717007506International Union of CrystallographyThe FELIX algorithm for indexing snaphot images containing multiple diffraction patterns is described and its performance is tested.enSERIAL CRYSTALLOGRAPHY; SFX; MATERIALS SCIENCE; STRUCTURAL BIOLOGYA novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues–Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on (\overline 110) facets.text/htmlFELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction imagestext4502017-07-07Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1075med@iucr.orgAugust 201710831600-5767How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal
http://scripts.iucr.org/cgi-bin/paper?gj5178
Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Porta, J.Lovelace, J.Borgstahl, G.E.O.2017-06-30doi:10.1107/S1600576717007294International Union of Crystallography(3 + 1)-dimensional superspace groups are explained for incommensurately modulated macromolecular crystals with an example.enPROTEIN X-RAY CRYSTALLOGRAPHY; APERIODIC CRYSTALS; INCOMMENSURATE MODULATION; SUPERSPACE GROUPSPeriodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal.text/htmlHow to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystaltext4502017-06-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767teaching and education1200med@iucr.orgAugust 201712071600-5767X-ray topography of subsurface crystal layers
http://scripts.iucr.org/cgi-bin/paper?vc5006
New capabilities of the Berg–Barrett topographic method are demonstrated using a skew-asymmetric X-ray diffraction scheme for investigating structural changes near the surface of semiconductor materials. Specifying the X-ray extinction depth, the details of defects and strains are revealed with high resolution. Consequently, analysis of structural distortion of layers near the surface after various types of surface processing becomes more complete.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Swiatek, Z.Fodchuk, I.Zaplitnyy, R.2017-05-30doi:10.1107/S1600576717007208International Union of CrystallographyThe practical application of the modified Berg–Barrett topographic method in a skew asymmetric scheme of X-ray diffraction is presented. The method is used for the study of the defect structure of CdTe crystals and Cd1−xHgxTe/CdTe epitaxial layers after the influence of different external factors (ion implantation and etching).enX-RAY DIFFRACTION; X-RAY TOPOGRAPHY; STRUCTURAL DIAGNOSTICS; ION IMPLANTATION; BERG-BARRET METHODNew capabilities of the Berg–Barrett topographic method are demonstrated using a skew-asymmetric X-ray diffraction scheme for investigating structural changes near the surface of semiconductor materials. Specifying the X-ray extinction depth, the details of defects and strains are revealed with high resolution. Consequently, analysis of structural distortion of layers near the surface after various types of surface processing becomes more complete.text/htmlX-ray topography of subsurface crystal layerstext503http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2017-05-30727research papers1600-5767June 2017med@iucr.org7331600-5767Structure diagnostics of heterostructures and multi-layered systems by X-ray multiple diffraction
http://scripts.iucr.org/cgi-bin/paper?vh5076
This article presents the results of research on multi-layered heterostructures by a modified calculation technique of multiple X-ray diffraction. The AlxIn1−xSb heterostructure and a Zn(Mn)Se/GaAs(001) multi-layered system were used as models to specify conditions for cases of coincidental coplanar three-beam or coincidental noncoplanar four-beam X-ray diffraction. These conditions provide the means for a high-precision determination of lattice parameters and strain anisotropy in layers.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Borcha, M.Fodchuk, I.Solodkyi, M.Baidakova, M.2017-05-25doi:10.1107/S1600576717006574International Union of CrystallographyOpportunities of multi-beam X-ray diffraction are demonstrated for determination of lattice strains in heterostructures and multi-layered systems.enX-RAY MULTI-BEAM DIFFRACTION; LATTICE PARAMETERS; STRAIN; MULTI-LAYERED SYSTEMSThis article presents the results of research on multi-layered heterostructures by a modified calculation technique of multiple X-ray diffraction. The AlxIn1−xSb heterostructure and a Zn(Mn)Se/GaAs(001) multi-layered system were used as models to specify conditions for cases of coincidental coplanar three-beam or coincidental noncoplanar four-beam X-ray diffraction. These conditions provide the means for a high-precision determination of lattice parameters and strain anisotropy in layers.text/htmlStructure diagnostics of heterostructures and multi-layered systems by X-ray multiple diffractiontext503http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2017-05-25722research papers1600-5767June 2017med@iucr.org7261600-5767Reconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patterns
http://scripts.iucr.org/cgi-bin/paper?yr5017
Recently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such `sparse' frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand–maximize–compress; Loh & Elser (2009). Phys. Rev. E, 80, 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Lan, T.-Y.Wierman, J.L.Tate, M.W.Philipp, H.T.Elser, V.Gruner, S.M.2017-06-14doi:10.1107/S1600576717006537International Union of CrystallographyTo simulate the signal level of serial microcrystallography experiments at storage ring sources, data frames were collected from a large lysozyme crystal rotated about two orthogonal axes and illuminated by a dim X-ray source. Using the EMC algorithm, this study shows that three-dimensional intensity reconstruction is still feasible even without the knowledge of the crystal orientation in each data frame.enX-RAY SERIAL MICROCRYSTALLOGRAPHY; SPARSE DATA; EMC ALGORITHM; PROTEIN MICROCRYSTALLOGRAPHY; SYNCHROTRON RADIATION SOURCESRecently, there has been a growing interest in adapting serial microcrystallography (SMX) experiments to existing storage ring (SR) sources. For very small crystals, however, radiation damage occurs before sufficient numbers of photons are diffracted to determine the orientation of the crystal. The challenge is to merge data from a large number of such `sparse' frames in order to measure the full reciprocal space intensity. To simulate sparse frames, a dataset was collected from a large lysozyme crystal illuminated by a dim X-ray source. The crystal was continuously rotated about two orthogonal axes to sample a subset of the rotation space. With the EMC algorithm [expand–maximize–compress; Loh & Elser (2009). Phys. Rev. E, 80, 026705], it is shown that the diffracted intensity of the crystal can still be reconstructed even without knowledge of the orientation of the crystal in any sparse frame. Moreover, parallel computation implementations were designed to considerably improve the time and memory scaling of the algorithm. The results show that EMC-based SMX experiments should be feasible at SR sources.text/htmlReconstructing three-dimensional protein crystal intensities from sparse unoriented two-axis X-ray diffraction patternstext4502017-06-14Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers985med@iucr.orgAugust 20179931600-5767An in situ USAXS–SAXS–WAXS study of precipitate size distribution evolution in a model Ni-based alloy
http://scripts.iucr.org/cgi-bin/paper?vh5072
Intermetallic γ′ precipitates typically strengthen nickel-based superalloys. The shape, size and spatial distribution of strengthening precipitates critically influence alloy strength, while their temporal evolution characteristics determine the high-temperature alloy stability. Combined ultra-small-, small- and wide-angle X-ray scattering (USAXS–SAXS–WAXS) analysis can be used to evaluate the temporal evolution of an alloy's precipitate size distribution (PSD) and phase structure during in situ heat treatment. Analysis of PSDs from USAXS–SAXS data employs either least-squares fitting of a preordained PSD model or a maximum entropy (MaxEnt) approach, the latter avoiding a priori definition of a functional form of the PSD. However, strong low-q scattering from grain boundaries and/or structure factor effects inhibit MaxEnt analysis of typical alloys. This work describes the extension of Bayesian–MaxEnt analysis methods to data exhibiting structure factor effects and low-q power law slopes and demonstrates their use in an in situ study of precipitate size evolution during heat treatment of a model Ni–Al–Si alloy.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Andrews, R.N.Serio, J.Muralidharan, G.Ilavsky, J.2017-05-30doi:10.1107/S1600576717006446International Union of CrystallographyCombined ultra-small-, small- and wide-angle X-ray scattering (USAXS–SAXS–WAXS) provides in situ evaluation of the precipitate size distribution (PSD) and phase structure temporal evolution during heat treatment. A method for extraction of an arbitrary PSD in the presence of interparticle interactions is described and illustrated for study of PSD evolution.enULTRA-SMALL-ANGLE X-RAY SCATTERING; SMALL-ANGLE X-RAY SCATTERING; WIDE-ANGLE X-RAY SCATTERING; USAXS-SAXS-WAXS; PRECIPITATION HARDENING; BAYESIAN INVERSE TRANSFORMATIONIntermetallic γ′ precipitates typically strengthen nickel-based superalloys. The shape, size and spatial distribution of strengthening precipitates critically influence alloy strength, while their temporal evolution characteristics determine the high-temperature alloy stability. Combined ultra-small-, small- and wide-angle X-ray scattering (USAXS–SAXS–WAXS) analysis can be used to evaluate the temporal evolution of an alloy's precipitate size distribution (PSD) and phase structure during in situ heat treatment. Analysis of PSDs from USAXS–SAXS data employs either least-squares fitting of a preordained PSD model or a maximum entropy (MaxEnt) approach, the latter avoiding a priori definition of a functional form of the PSD. However, strong low-q scattering from grain boundaries and/or structure factor effects inhibit MaxEnt analysis of typical alloys. This work describes the extension of Bayesian–MaxEnt analysis methods to data exhibiting structure factor effects and low-q power law slopes and demonstrates their use in an in situ study of precipitate size evolution during heat treatment of a model Ni–Al–Si alloy.text/htmlAn in situ USAXS–SAXS–WAXS study of precipitate size distribution evolution in a model Ni-based alloytext503http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2017-05-30734research papers1600-5767June 2017med@iucr.org7401600-5767CrystalWalk: crystal structures, step by step
http://scripts.iucr.org/cgi-bin/paper?ks5568
CrystalWalk is a crystal editor and visualization software designed for teaching materials science and engineering. Based on WebGL/HTML5, it provides an accessible and interactive platform to students and teachers by introducing a simplified crystallographic approach that creates crystal structures by combining a lattice with a motif without the use of its internal symmetry. CrystalWalk is the first software to use solely translational symmetry, aiming to introduce engineering students to the basic concepts of lattice and motif. Although very restrictive from the crystallographic point of view, CrystalWalk makes it simple for students to experiment, reproduce and visualize, in an interactive manner, most of the crystal structures that are commonly introduced in materials science and engineering curricula.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Bardella, F.Montes Rodrigues, A.Leal Neto, R.M.2017-05-25doi:10.1107/S160057671700560XInternational Union of CrystallographyCrystalWalk is a crystal editor and visualization software designed for teaching materials science and engineering. Based on WebGL/HTML5, it provides an accessible and interactive platform to students, teachers and researchers.enCRYSTAL STRUCTURE SYNTHESIS; CRYSTAL STRUCTURE VISUALIZATION; MATERIALS SCIENCE TEACHING; EDUCATIONAL SOFTWARECrystalWalk is a crystal editor and visualization software designed for teaching materials science and engineering. Based on WebGL/HTML5, it provides an accessible and interactive platform to students and teachers by introducing a simplified crystallographic approach that creates crystal structures by combining a lattice with a motif without the use of its internal symmetry. CrystalWalk is the first software to use solely translational symmetry, aiming to introduce engineering students to the basic concepts of lattice and motif. Although very restrictive from the crystallographic point of view, CrystalWalk makes it simple for students to experiment, reproduce and visualize, in an interactive manner, most of the crystal structures that are commonly introduced in materials science and engineering curricula.text/htmlCrystalWalk: crystal structures, step by steptext503Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallography2017-05-25949teaching and education1600-5767June 2017med@iucr.org9501600-5767Single-shot full strain tensor determination with microbeam X-ray Laue diffraction and a two-dimensional energy-dispersive detector
http://scripts.iucr.org/cgi-bin/paper?ks5549
The full strain and stress tensor determination in a triaxially stressed single crystal using X-ray diffraction requires a series of lattice spacing measurements at different crystal orientations. This can be achieved using a tunable X-ray source. This article reports on a novel experimental procedure for single-shot full strain tensor determination using polychromatic synchrotron radiation with an energy range from 5 to 23 keV. Microbeam X-ray Laue diffraction patterns were collected from a copper micro-bending beam along the central axis (centroid of the cross section). Taking advantage of a two-dimensional energy-dispersive X-ray detector (pnCCD), the position and energy of the collected Laue spots were measured for multiple positions on the sample, allowing the measurement of variations in the local microstructure. At the same time, both the deviatoric and hydrostatic components of the elastic strain and stress tensors were calculated.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Abboud, A.Kirchlechner, C.Keckes, J.Conka Nurdan, T.Send, S.Micha, J.S.Ulrich, O.Hartmann, R.Strüder, L.Pietsch, U.2017-05-30doi:10.1107/S1600576717005581International Union of CrystallographyBy simultaneously measuring changes in energy and reflection angle of Laue spots with respect to a reference position, it is possible to measure all lattice parameters of a unit cell and calculate the full strain/stress tensors in a single-shot experiment with high spatial resolution.enSTRAIN; MICROBEAM X-RAY LAUE DIFFRACTION; ENERGY-DISPERSIVE X-RAY DETECTORSThe full strain and stress tensor determination in a triaxially stressed single crystal using X-ray diffraction requires a series of lattice spacing measurements at different crystal orientations. This can be achieved using a tunable X-ray source. This article reports on a novel experimental procedure for single-shot full strain tensor determination using polychromatic synchrotron radiation with an energy range from 5 to 23 keV. Microbeam X-ray Laue diffraction patterns were collected from a copper micro-bending beam along the central axis (centroid of the cross section). Taking advantage of a two-dimensional energy-dispersive X-ray detector (pnCCD), the position and energy of the collected Laue spots were measured for multiple positions on the sample, allowing the measurement of variations in the local microstructure. At the same time, both the deviatoric and hydrostatic components of the elastic strain and stress tensors were calculated.text/htmlSingle-shot full strain tensor determination with microbeam X-ray Laue diffraction and a two-dimensional energy-dispersive detectortext503http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2017-05-30901research papers1600-5767June 2017med@iucr.org9081600-5767Instrumental resolution as a function of scattering angle and wavelength as exemplified for the POWGEN instrument
http://scripts.iucr.org/cgi-bin/paper?pd5090
The method of angular- and wavelength-dispersive (e.g. two-dimensional) Rietveld refinement is a new and emerging tool for the analysis of neutron diffraction data measured at time-of-flight instruments with large area detectors. Following the approach for one-dimensional refinements (using either scattering angle or time of flight), the first step at each beam time cycle is the calibration of the instrument including the determination of instrumental contributions to the peak shape variation to be expected for diffraction patterns measured by the users. The aim of this work is to provide the users with calibration files and – for the later Rietveld refinement of the measured data – with an instrumental resolution file (IRF). This article will elaborate on the necessary steps to generate such an IRF for the angular- and wavelength-dispersive case, exemplified for the POWGEN instrument. A dataset measured on a standard diamond sample is used to extract the profile function in the two-dimensional case. It is found that the variation of reflection width with 2θ and λ can be expressed by the standard equation used for evaluating the instrumental resolution, which yields a substantially more fundamental approach to the parameterization of the instrumental contribution to the peak shape. Geometrical considerations of the POWGEN instrument and sample effects lead to values for Δθ, Δt and ΔL that yield a very good match to the extracted FWHM values. In a final step the refinement results are compared with the one-dimensional, i.e. diffraction-focused, case.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Jacobs, P.Houben, A.Schweika, W.Tchougréeff, A.L.Dronskowski, R.2017-05-25doi:10.1107/S1600576717005398International Union of CrystallographyA fundamental description of the instrument resolution file is elaborated for the angular- and wavelength-dispersive cases of Rietveld refinement, exemplified for the POWGEN instrument. It is shown how to refine the necessary profile function parameters from a dataset measured on a diamond reference sample. The analysis is performed in a two-dimensional refinement space based on the convenient variables d and d⊥.enINSTRUMENTAL RESOLUTION; POWGEN; TIME OF FLIGHT; NEUTRON DIFFRACTION; ANGULAR- AND WAVELENGTH-DISPERSIVE RIETVELD REFINEMENT; POWDER METHODSThe method of angular- and wavelength-dispersive (e.g. two-dimensional) Rietveld refinement is a new and emerging tool for the analysis of neutron diffraction data measured at time-of-flight instruments with large area detectors. Following the approach for one-dimensional refinements (using either scattering angle or time of flight), the first step at each beam time cycle is the calibration of the instrument including the determination of instrumental contributions to the peak shape variation to be expected for diffraction patterns measured by the users. The aim of this work is to provide the users with calibration files and – for the later Rietveld refinement of the measured data – with an instrumental resolution file (IRF). This article will elaborate on the necessary steps to generate such an IRF for the angular- and wavelength-dispersive case, exemplified for the POWGEN instrument. A dataset measured on a standard diamond sample is used to extract the profile function in the two-dimensional case. It is found that the variation of reflection width with 2θ and λ can be expressed by the standard equation used for evaluating the instrumental resolution, which yields a substantially more fundamental approach to the parameterization of the instrumental contribution to the peak shape. Geometrical considerations of the POWGEN instrument and sample effects lead to values for Δθ, Δt and ΔL that yield a very good match to the extracted FWHM values. In a final step the refinement results are compared with the one-dimensional, i.e. diffraction-focused, case.text/htmlInstrumental resolution as a function of scattering angle and wavelength as exemplified for the POWGEN instrumenttext503http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2017-05-25866research papers1600-5767June 2017med@iucr.org8751600-5767The ash heap of crystallography: restoring forgotten basic knowledge. Corrigendum
http://scripts.iucr.org/cgi-bin/paper?gj9135
One imprecise and one incomplete statement in the article by Nespolo [J. Appl. Cryst. (2015), 48, 1290–1298] are corrected.Copyright (c) 2017 International Union of Crystallographyurn:issn:1600-5767Nespolo, M.2017-04-27doi:10.1107/S1600576717006306International Union of CrystallographyOne imprecise and one incomplete statement in the article by Nespolo [J. Appl. Cryst. (2015), 48, 1290–1298] are corrected.enCRYSTAL FORMS; SYSTEMATIC ABSENCES; MILLER INDICES; SYMMETRY RESTRICTIONS; CRYSTALLOGRAPHIC EDUCATIONOne imprecise and one incomplete statement in the article by Nespolo [J. Appl. Cryst. (2015), 48, 1290–1298] are corrected.text/htmlThe ash heap of crystallography: restoring forgotten basic knowledge. Corrigendumtext503Copyright (c) 2017 International Union of CrystallographyJournal of Applied Crystallography2017-04-27978addenda and errata1600-5767June 2017med@iucr.org9791600-5767Interface-sensitive imaging by an image reconstruction aided X-ray reflectivity technique
http://scripts.iucr.org/cgi-bin/paper?vc5005
Recently, the authors have succeeded in realizing X-ray reflectivity imaging of heterogeneous ultrathin films at specific wavevector transfers by applying a wide parallel beam and an area detector. By combining in-plane angle and grazing-incidence angle scans, it is possible to reconstruct a series of interface-sensitive X-ray reflectivity images at different grazing-incidence angles (proportional to wavevector transfers). The physical meaning of a reconstructed X-ray reflectivity image at a specific wavevector transfer is the two-dimensional reflectivity distribution of the sample. In this manner, it is possible to retrieve the micro-X-ray reflectivity (where the pixel size is on the microscale) profiles at different local positions on the sample.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Jiang, J.Hirano, K.Sakurai, K.2017-05-25doi:10.1107/S160057671700509XInternational Union of CrystallographyThis article describes interface-sensitive imaging of heterogeneous thin films by an image reconstruction aided X-ray reflectivity technique with an 8 mm-wide parallel beam; the possibility of extracting micro-X-ray reflectivity profiles from the same data collection is discussed.enSURFACES AND INTERFACES; MICRO-IMAGING; X-RAY REFLECTIVITY; IMAGE RECONSTRUCTION; VISUALIZATIONRecently, the authors have succeeded in realizing X-ray reflectivity imaging of heterogeneous ultrathin films at specific wavevector transfers by applying a wide parallel beam and an area detector. By combining in-plane angle and grazing-incidence angle scans, it is possible to reconstruct a series of interface-sensitive X-ray reflectivity images at different grazing-incidence angles (proportional to wavevector transfers). The physical meaning of a reconstructed X-ray reflectivity image at a specific wavevector transfer is the two-dimensional reflectivity distribution of the sample. In this manner, it is possible to retrieve the micro-X-ray reflectivity (where the pixel size is on the microscale) profiles at different local positions on the sample.text/htmlInterface-sensitive imaging by an image reconstruction aided X-ray reflectivity techniquetext503http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2017-05-25712research papers1600-5767June 2017med@iucr.org7211600-5767