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Universal parameters of bulk-solvent masks. 块状溶剂掩膜的通用参数。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-02-09 DOI: 10.1107/S2053273324000299
Alexandre Urzhumtsev, Paul Adams, Pavel Afonine
{"title":"Universal parameters of bulk-solvent masks.","authors":"Alexandre Urzhumtsev, Paul Adams, Pavel Afonine","doi":"10.1107/S2053273324000299","DOIUrl":"10.1107/S2053273324000299","url":null,"abstract":"<p><p>The bulk solvent is a major component of biomacromolecular crystals that contributes significantly to the observed diffraction intensities. Accurate modelling of the bulk solvent has been recognized as important for many crystallographic calculations. Owing to its simplicity and modelling power, the flat (mask-based) bulk-solvent model is used by most modern crystallographic software packages to account for disordered solvent. In this model, the bulk-solvent contribution is defined by a binary mask and a scale (scattering) function. The mask is calculated on a regular grid using the atomic model coordinates and their chemical types. The grid step and two radii, solvent and shrinkage, are the three parameters that govern the mask calculation. They are highly correlated and their choice is a compromise between the computer time needed to calculate the mask and the accuracy of the mask. It is demonstrated here that this choice can be optimized using a unique value of 0.6 Å for the grid step irrespective of the data resolution, and the radii values adjusted correspondingly. The improved values were tested on a large sample of Protein Data Bank entries derived from X-ray diffraction data and are now used in the computational crystallography toolbox (CCTBX) and in Phenix as the default choice.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"194-201"},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139705389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Report of the Executive Committee for 2022. 2022 年执行委员会报告。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-02-22 DOI: 10.1107/S2053273323008197
{"title":"Report of the Executive Committee for 2022.","authors":"","doi":"10.1107/S2053273323008197","DOIUrl":"10.1107/S2053273323008197","url":null,"abstract":"<p><p>The report of the Executive Committee for 2022 is presented.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"221-223"},"PeriodicalIF":1.8,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139928976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modelling dynamical 3D electron diffraction intensities. I. A scattering cluster algorithm. 动态三维电子衍射强度建模。I. 散射群算法。
IF 1.9 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-03-01 Epub Date: 2024-01-25 DOI: 10.1107/S2053273323010689
Budhika Mendis
{"title":"Modelling dynamical 3D electron diffraction intensities. I. A scattering cluster algorithm.","authors":"Budhika Mendis","doi":"10.1107/S2053273323010689","DOIUrl":"10.1107/S2053273323010689","url":null,"abstract":"<p><p>Three-dimensional electron diffraction (3D-ED) is a powerful technique for crystallographic characterization of nanometre-sized crystals that are too small for X-ray diffraction. For accurate crystal structure refinement, however, it is important that the Bragg diffracted intensities are treated dynamically. Bloch wave simulations are often used in 3D-ED, but can be computationally expensive for large unit cell crystals due to the large number of diffracted beams. Proposed here is an alternative method, the `scattering cluster algorithm' (SCA), that replaces the eigen-decomposition operation in Bloch waves with a simpler matrix multiplication. The underlying principle of SCA is that the intensity of a given Bragg reflection is largely determined by intensity transfer (i.e. `scattering') from a cluster of neighbouring diffracted beams. However, the penalty for using matrix multiplication is that the sample must be divided into a series of thin slices and the diffracted beams calculated iteratively, similar to the multislice approach. Therefore, SCA is more suitable for thin specimens. The accuracy and speed of SCA are demonstrated on tri-isopropyl silane (TIPS) pentacene and rubrene, two exemplar organic materials with large unit cells.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"167-177"},"PeriodicalIF":1.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10913674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139544987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Analytical models representing X-ray form factors of ions. 代表离子 X 射线形式因子的分析模型。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323010550
Gunnar Thorkildsen
{"title":"Analytical models representing X-ray form factors of ions.","authors":"Gunnar Thorkildsen","doi":"10.1107/S2053273323010550","DOIUrl":"10.1107/S2053273323010550","url":null,"abstract":"<p><p>Parameters in analytical models for X-ray form factors of ions f<sub>0</sub>(s), based on the inverse Mott-Bethe formula involving a variable number of Gaussians, are determined for a wide range of published data sets {s, f<sub>0</sub>(s)}. The models reproduce the calculated form-factor values close to what is expected from a uniform statistical distribution with limits determined by their precision. For different ions associated with the same atom, the number of Gaussians in the models decreases with increasing net positive charge.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"129-136"},"PeriodicalIF":1.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10833360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139072707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Maximal independence and symmetry in crystal chemistry of natural tectosilicates. 天然构造硅酸盐晶体化学的最大独立性和对称性。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323008665
Montauban Moreira de Oliveira, Jean Guillaume Eon
{"title":"Maximal independence and symmetry in crystal chemistry of natural tectosilicates.","authors":"Montauban Moreira de Oliveira, Jean Guillaume Eon","doi":"10.1107/S2053273323008665","DOIUrl":"10.1107/S2053273323008665","url":null,"abstract":"<p><p>Löwenstein's avoidance rule in aluminosilicates is reinterpreted on the basis of the fourth Pauling rule. It is shown that avoidance of Si-O-Si bridges may account for avoidance of Al-O-Al bridges. In view of this interpretation, it is proposed that the most favourable distributions of cations entering in substitution of silicon in the framework are associated to maximal independent sets of the respective 3-periodic nets. Among all possible solutions, only those with maximal symmetry are realized. The applicability of the concept is demonstrated for a few natural tectosilicates, which have been analysed through the prism of their labelled quotient graph.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"52-64"},"PeriodicalIF":1.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89716121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Symmetry groups of two-way twofold and three-way threefold fabrics. 双向两折和三向三折织物的对称群。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323008938
Ma Louise Antonette De Las Peñas, Mark Tomenes, Kristan Liza
{"title":"Symmetry groups of two-way twofold and three-way threefold fabrics.","authors":"Ma Louise Antonette De Las Peñas, Mark Tomenes, Kristan Liza","doi":"10.1107/S2053273323008938","DOIUrl":"10.1107/S2053273323008938","url":null,"abstract":"<p><p>This work discusses the symmetry groups of two classes of woven fabrics, two-way twofold fabrics and three-way threefold fabrics. A method to arrive at a design of a fabric is presented, employing methods in color symmetry theory. Geometric representations of all possible layer group or diperiodic symmetry structures of the fabrics are derived. There are 50 layer symmetry groups corresponding to two-way twofold fabrics and 27 layer symmetry groups corresponding to three-way threefold fabrics.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"33-51"},"PeriodicalIF":1.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138795871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Realizations of crystal nets. I. (Generalized) derived graphs. 水晶网的实现。I. （广义）派生图。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S205327332300949X
Gregory McColm
{"title":"Realizations of crystal nets. I. (Generalized) derived graphs.","authors":"Gregory McColm","doi":"10.1107/S205327332300949X","DOIUrl":"10.1107/S205327332300949X","url":null,"abstract":"<p><p>A crystal net can be derived from a `generalized' voltage graph representing a graph analog of a fundamental domain of that crystal net along with a sufficient collection of its symmetries. The voltage assignments include not only isometries to the (oriented) edges, but also `weight' groups assigned to vertices for generating the vertex figures around those vertices. By varying the voltage assignments, one obtains geometrically distinct - and occasionally topologically distinct - Euclidean graphs. The focus here is on deriving simple graphs, i.e. graphs with no loops or lunes, especially uninodal edge transitive graphs.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"18-32"},"PeriodicalIF":1.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138795870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Periodic Borromean rings, rods and chains. 周期波罗米安环，杆和链。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323009269
Michael O'Keeffe, Michael M J Treacy
{"title":"Periodic Borromean rings, rods and chains.","authors":"Michael O'Keeffe, Michael M J Treacy","doi":"10.1107/S2053273323009269","DOIUrl":"10.1107/S2053273323009269","url":null,"abstract":"<p><p>This article describes periodic polycatenane structures built from interlocked rings in which no two are directly linked. The 2-periodic vertex-, edge- and ring-transitive families of hexagonal Borromean rings are described in detail, and it is shown how these give rise to 1- and 3-periodic ring-transitive (isonemal) families. A second isonemal 2-periodic family is identified, as is a unique 3-periodic Borromean assembly of equilateral triangles. Also reported is a notable 2-periodic structure comprising chains of linked rings in which the chains are locked in place but no two chains are directly interlinked, being held in place as a novel `quasi-Borromean' set of four repeating components.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"79-85"},"PeriodicalIF":1.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Periodic diffraction from an aperiodic monohedral tiling. 非周期单面体平铺的周期性衍射。
IF 1.9 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323009506
Craig S Kaplan, Michael O'Keeffe, Michael M J Treacy
{"title":"Periodic diffraction from an aperiodic monohedral tiling.","authors":"Craig S Kaplan, Michael O'Keeffe, Michael M J Treacy","doi":"10.1107/S2053273323009506","DOIUrl":"10.1107/S2053273323009506","url":null,"abstract":"<p><p>The diffraction pattern from the recently reported aperiodic `einstein', or `hat', monohedral tiling [Smith et al. (2023). arXiv:2303.10798v1] has been analyzed. The structure is the hexagonal mta net, a kite tiling, with aperiodic vertex deletions. A large model's diffraction pattern displays a robust sixfold periodicity in plane group p6. A repeating, roughly triangular motif of `diffused intensity' arises between the strongest Bragg peaks. The motif contains high-density regions of discrete `satellite' peaks, rather than continuous `diffuse scattering', breaking mirror symmetry, consistent with the chiral hat tiling.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"72-78"},"PeriodicalIF":1.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138497223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Algorithm for spin symmetry operation search. 自旋对称运算搜索算法。
IF 1.8 4区 材料科学
Acta Crystallographica Section A: Foundations and Advances Pub Date : 2024-01-01 DOI: 10.1107/S2053273323009257
Kohei Shinohara, Atsushi Togo, Hikaru Watanabe, Takuya Nomoto, Isao Tanaka, Ryotaro Arita
{"title":"Algorithm for spin symmetry operation search.","authors":"Kohei Shinohara, Atsushi Togo, Hikaru Watanabe, Takuya Nomoto, Isao Tanaka, Ryotaro Arita","doi":"10.1107/S2053273323009257","DOIUrl":"10.1107/S2053273323009257","url":null,"abstract":"<p><p>A spin space group provides a suitable way of fully exploiting the symmetry of a spin arrangement with a negligible spin-orbit coupling. There has been a growing interest in applying spin symmetry analysis with the spin space group in the field of magnetism. However, there is no established algorithm to search for spin symmetry operations of the spin space group. This paper presents an exhaustive algorithm for determining the spin symmetry operations of commensurate spin arrangements. The present algorithm searches for spin symmetry operations from the symmetry operations of a corresponding nonmagnetic crystal structure and determines their spin-rotation parts by solving a Procrustes problem. An implementation is distributed under a permissive free software license in spinspg Version 0.1.1, available at https://github.com/spglib/spinspg.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"94-103"},"PeriodicalIF":1.8,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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