Acta Crystallographica Section A最新文献_第9页

The superstructure determination of displacive distortions via symmetry-mode analysis. 上部结构位移变形的对称模态分析。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-01-05 DOI: 10.1107/S0108767311046241

Sean Kerman, Branton J Campbell, Kiran K Satyavarapu, Harold T Stokes, Francesca Perselli, John S O Evans

{"title":"The superstructure determination of displacive distortions via symmetry-mode analysis.","authors":"Sean Kerman, Branton J Campbell, Kiran K Satyavarapu, Harold T Stokes, Francesca Perselli, John S O Evans","doi":"10.1107/S0108767311046241","DOIUrl":"https://doi.org/10.1107/S0108767311046241","url":null,"abstract":"For any crystal structure that can be viewed as a low-symmetry distortion of some higher-symmetry parent structure, one can represent the details of the distorted structure in terms of symmetry-adapted distortion modes of the parent structure rather than the traditional list of atomic xyz coordinates. Because most symmetry modes tend to be inactive, and only a relatively small number of mode amplitudes are dominant in producing the observed distortion, symmetry-mode analysis can greatly simplify the determination of a displacively distorted structure from powder diffraction data. This is an important capability when peak splittings are small, superlattice intensities are weak or systematic absences fail to distinguish between candidate symmetries. Here, the symmetry-mode basis is treated as a binary (on/off) parameter set that spans the space of all possible P1 symmetry distortions within the experimentally determined supercell. Using the average R(wp) over repeated local minimizations from random starting points as a cost function for a given mode set, global search strategies are employed to identify the active modes of the distortion. This procedure automatically yields the amplitudes of the active modes and the associated atomic coordinates. The active modes are then used to detect the space-group symmetry of the distorted phase (i.e. the type and location of each of the parent symmetry elements that remain within the distorted supercell). Once a handful of active modes are identified, traditional refinement methods readily yield their amplitudes and the resulting atomic coordinates. A final symmetry-mode refinement is then performed in the correct space-group symmetry to improve the sensitivity to any secondary modes present.","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 2","pages":"222-34"},"PeriodicalIF":1.8,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767311046241","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30463172","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: 21

Covariance and correlation estimation in electron-density maps. 电子密度图中的协方差和相关估计。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-01-25 DOI: 10.1107/S0108767311053281

Angela Altomare, Corrado Cuocci, Carmelo Giacovazzo, Anna Moliterni, Rosanna Rizzi

{"title":"Covariance and correlation estimation in electron-density maps.","authors":"Angela Altomare, Corrado Cuocci, Carmelo Giacovazzo, Anna Moliterni, Rosanna Rizzi","doi":"10.1107/S0108767311053281","DOIUrl":"https://doi.org/10.1107/S0108767311053281","url":null,"abstract":"Quite recently two papers have been published [Giacovazzo & Mazzone (2011). Acta Cryst. A67, 210-218; Giacovazzo et al. (2011). Acta Cryst. A67, 368-382] which calculate the variance in any point of an electron-density map at any stage of the phasing process. The main aim of the papers was to associate a standard deviation to each pixel of the map, in order to obtain a better estimate of the map reliability. This paper deals with the covariance estimate between points of an electron-density map in any space group, centrosymmetric or non-centrosymmetric, no matter the correlation between the model and target structures. The aim is as follows: to verify if the electron density in one point of the map is amplified or depressed as an effect of the electron density in one or more other points of the map. High values of the covariances are usually connected with undesired features of the map. The phases are the primitive random variables of our probabilistic model; the covariance changes with the quality of the model and therefore with the quality of the phases. The conclusive formulas show that the covariance is also influenced by the Patterson map. Uncertainty on measurements may influence the covariance, particularly in the final stages of the structure refinement; a general formula is obtained taking into account both phase and measurement uncertainty, valid at any stage of the crystal structure solution.","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 2","pages":"244-55"},"PeriodicalIF":1.8,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767311053281","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30464197","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: 4

Higher-dimensional crystallography of N-fold quasiperiodic tilings. n叠准周期瓷砖的高维晶体学。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-02-08 DOI: 10.1107/S0108767312001705

Sofia Deloudi, Walter Steurer

引用次数: 3

Frequency distribution of the reduced unit cells of centred lattices from the Protein Data Bank. 蛋白质数据库中中心格的约简单位细胞的频率分布。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-01-12 DOI: 10.1107/S0108767311052263

Kunchithapadam Swaminathan

引用次数: 1

Quantitative crystal structure descriptors from multiplicative congruential generators. 从乘法同余生成的定量晶体结构描述符。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-01-12 DOI: 10.1107/S0108767311049853

Wolfgang Hornfeck

{"title":"Quantitative crystal structure descriptors from multiplicative congruential generators.","authors":"Wolfgang Hornfeck","doi":"10.1107/S0108767311049853","DOIUrl":"https://doi.org/10.1107/S0108767311049853","url":null,"abstract":"Special types of number-theoretic relations, termed multiplicative congruential generators (MCGs), exhibit an intrinsic sublattice structure. This has considerable implications within the crystallographic realm, namely for the coordinate description of crystal structures for which MCGs allow for a concise way of encoding the numerical structural information. Thus, a conceptual framework is established, with some focus on layered superstructures, which proposes the use of MCGs as a tool for the quantitative description of crystal structures. The multiplicative congruential method eventually affords an algorithmic generation of three-dimensional crystal structures with a near-uniform distribution of atoms, whereas a linearization procedure facilitates their combinatorial enumeration and classification. The outlook for homometric structures and dual-space crystallography is given. Some generalizations and extensions are formulated in addition, revealing the connections of MCGs with geometric algebra, discrete dynamical systems (iterative maps), as well as certain quasicrystal approximants.","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 2","pages":"167-80"},"PeriodicalIF":1.8,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767311049853","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30463167","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: 5

Image formation in the scanning transmission electron microscope using object-conjugate detectors. 用物体共轭检测器在扫描透射电子显微镜中成像。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-01-12 DOI: 10.1107/S0108767311051592

C Dwyer, S Lazar, L Y Chang, J Etheridge

{"title":"Image formation in the scanning transmission electron microscope using object-conjugate detectors.","authors":"C Dwyer, S Lazar, L Y Chang, J Etheridge","doi":"10.1107/S0108767311051592","DOIUrl":"https://doi.org/10.1107/S0108767311051592","url":null,"abstract":"This work presents a theoretical analysis of image formation in a scanning transmission electron microscope equipped with electron detectors in a plane conjugate to the specimen. This optical geometry encompasses both the three-dimensional imaging technique of scanning confocal electron microscopy (SCEM) and a recently developed atomic resolution imaging technique coined real-space scanning transmission electron microscopy (R-STEM). Image formation in this geometry is considered from the viewpoints of both wave optics and geometric optics, and the validity of the latter is analysed by means of Wigner distributions. Relevant conditions for the validity of a geometric interpretation of image formation are provided. For R-STEM, where a large detector is used, it is demonstrated that a geometric optics description of image formation provides an accurate approximation to wave optics, and that this description offers distinct advantages for interpretation and numerical implementation. The resulting description of R-STEM is also demonstrated to be in good agreement with experiment. For SCEM, it is emphasized that a geometric optics description of image formation is valid provided that higher-order aberrations can be ignored and the detector size is large enough to average out diffraction from the angle-limiting aperture.","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 2","pages":"196-207"},"PeriodicalIF":1.8,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767311051592","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30463170","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: 4

Mathematical aspects of molecular replacement. II. Geometry of motion spaces. 分子置换的数学方面。2运动空间的几何学。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-02-07 DOI: 10.1107/S010876731105118X

Gregory S Chirikjian, Yan Yan

引用次数: 13

Computation of small-angle scattering profiles with three-dimensional Zernike polynomials. 用三维Zernike多项式计算小角度散射剖面。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-02-09 DOI: 10.1107/S010876731104788X

Haiguang Liu, Richard J Morris, Alexander Hexemer, Scott Grandison, Peter H Zwart

引用次数: 52

On the significance of Bragg reflections. 论布拉格反射的意义。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-02-16 DOI: 10.1107/S0108767312003066

Mads Ry Vogel Jørgensen, Helle Svendsen, Mette Stokkebro Schmøkel, Jacob Overgaard, Bo Brummerstedt Iversen

{"title":"On the significance of Bragg reflections.","authors":"Mads Ry Vogel Jørgensen, Helle Svendsen, Mette Stokkebro Schmøkel, Jacob Overgaard, Bo Brummerstedt Iversen","doi":"10.1107/S0108767312003066","DOIUrl":"https://doi.org/10.1107/S0108767312003066","url":null,"abstract":"Recently Henn & Meindl [Acta Cryst. (2010), A66, 676-684] examined the significance of Bragg diffraction data through the descriptor W = (I(1/2))/(σ(I)). In the Poisson limit for the intensity errors W equals unity, but any kind of data processing (background subtraction, integration, scaling, absorption correction, Lorentz and polarization correction etc.) introduces additional error as well as remaining systematic errors and thus the significance of processed Bragg diffraction data is expected to be below the Poisson limit (W(Bragg) < 1). Curiously, it was observed by Henn & Meindl for several data sets that W(Bragg) had values larger than one. In the present study this is shown to be an artefact due to the neglect of a data scale factor applied to the standard uncertainties, and corrected values of W(Bragg) applied to Bragg data on an absolute scale are presented, which are all smaller than unity. Furthermore, the error estimation models employed by two commonly used data-processing programs {SADABS (Bruker AXS Inc., Madison, Wisconsin, USA) and SORTAV [Blessing (1997). J. Appl. Cryst. 30, 421-426]} are examined. It is shown that the empirical error model in SADABS very significantly lowers the significance of the Bragg data and it also results in a very strange distributions of errors, as observed by Henn & Meindl. On the other hand, error estimation based on the variance of a population of abundant intensity data, as used in SORTAV, provides reasonable error estimates, which are only slightly less significant than the raw data. Given that modern area detectors make measurement of highly redundant data relatively straightforward, it is concluded that the latter is the best approach for processing of data.","PeriodicalId":7400,"journal":{"name":"Acta Crystallographica Section A","volume":"68 Pt 2","pages":"301-3; discussion 304"},"PeriodicalIF":1.8,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S0108767312003066","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30464204","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: 15

Phase retrieval in protein crystallography. 蛋白质晶体学中的相位检索。

IF 1.8 4区材料科学

Acta Crystallographica Section A Pub Date : 2012-03-01 Epub Date: 2012-02-07 DOI: 10.1107/S0108767311053815

Zhong Chuan Liu, Rui Xu, Yu Hui Dong

引用次数: 25