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Protein secondary-structure description with a coarse-grained model: code and datasets in ActivePapers format 粗粒度模型的蛋白质二级结构描述:ActivePapers格式的代码和数据集
Acta Crystallographica Pub Date : 2015-07-28 DOI: 10.5281/zenodo.21690
G. Kneller, K. Hinsen
{"title":"Protein secondary-structure description with a coarse-grained model: code and datasets in ActivePapers format","authors":"G. Kneller, K. Hinsen","doi":"10.5281/zenodo.21690","DOIUrl":"https://doi.org/10.5281/zenodo.21690","url":null,"abstract":"","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"24 1","pages":"1411-1422"},"PeriodicalIF":0.0,"publicationDate":"2015-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78218997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advances in Crystallographic Image Processing for Scanning Probe Microscopy 扫描探针显微镜晶体图像处理研究进展
Acta Crystallographica Pub Date : 2014-08-05 DOI: 10.1107/S2053273314083922
P. Moeck
{"title":"Advances in Crystallographic Image Processing for Scanning Probe Microscopy","authors":"P. Moeck","doi":"10.1107/S2053273314083922","DOIUrl":"https://doi.org/10.1107/S2053273314083922","url":null,"abstract":"This book chapter reviews progress in crystallographic image processing (CIP) for scanning probe microscopy (SPM) that has occurred since our description of the technique was first put into open access in this book series in the year 2010. The signal to noise ratio in all kinds of experimental images of more or less regular 2D periodic arrays is significantly enhanced by CIP and the technique is independent of the type of recording device. In the SPM imaging context, CIP can be understood as an a posteriori sharpening of the effective experimental scanning probe tip by computational means. It is now possible to remove multiple scanning probe mini-tip effects in images from 2D periodic arrays of physical objects that either self-assembled or were created artificially. Accepted within the scientific community is by now also the fact that SPM tips can change their shape and fine structure during the operation of a microscope and, thereby, obfuscate the recorded images in systematic ways. CIP restores much of the smeared out information in such images. The adaptation of a geometric Akaike Information Criterion from the robotics and computer vision community to the unambiguous detection of 2D translation symmetries enabled much of our recent progress. In the main body of this book chapter, we discuss this adaptation and briefly illustrate its utility on an example.","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74472966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
3D Printing of Crystallographic Models for Interdisciplinary College Education 跨学科大学教育结晶模型的3D打印
Acta Crystallographica Pub Date : 2014-08-05 DOI: 10.1107/S2053273314086203
P. Moeck, W. Kaminsky, Trevor J. Snyder
{"title":"3D Printing of Crystallographic Models for Interdisciplinary College Education","authors":"P. Moeck, W. Kaminsky, Trevor J. Snyder","doi":"10.1107/S2053273314086203","DOIUrl":"https://doi.org/10.1107/S2053273314086203","url":null,"abstract":"Crystallographic models of molecule and crystal structures, crystal morphologies, Bravais lattices, space and point group symmetries, highly local and extended crystal defects, ... can all be encoded in the Crystallographic Information Framework (CIF) file format. While 3D printing has been available for at least 20 years, cost and performance improvements have only recently made 3D printing practical for usage by college educators and the general public. There is also an industry wide 3D printing standard, the STL file format. Virtual reality freeware programs that include conversions from CIF to STL are openly available [1]. The more than 250,000 entries Crystallography Open Database (COD) has in recent years developed into the world’s premier open-access source for CIFs of structures of small molecules and small to medium sized unit cell crystals [2]. The International Advisory Board of the COD also supports a related project [3a], which provides CIFs for interdisciplinary college education. Three of these “COD offspring” databases have started to provide for free downloads of STL files of small molecules, crystal morphologies, and grain boundaries [3b]. These 3D printing files were created directly from the CIFs in these databases. It is now up to interested college educators to develop new pedagogy in teaching crystallography on the basis of 3D models that can be printed out from these files. To facilitate further developments in this field, there is a web portal of open-access crystallography resources to which all interested college educators are invited to contribute [3c].","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88726513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Supramolecular anion coordination networks with (6.3) cation-templated topologies 具有(6.3)阳离子模板拓扑的超分子阴离子配位网络
Acta Crystallographica Pub Date : 2008-08-23 DOI: 10.1107/S0108767308084286
G. Resnati, P. Metrangolo, F. Meyer, T. Pilati, Giancarlo Terraneo, C. Ticozzi
{"title":"Supramolecular anion coordination networks with (6.3) cation-templated topologies","authors":"G. Resnati, P. Metrangolo, F. Meyer, T. Pilati, Giancarlo Terraneo, C. Ticozzi","doi":"10.1107/S0108767308084286","DOIUrl":"https://doi.org/10.1107/S0108767308084286","url":null,"abstract":"1 etc. We are looking in particular for supramolecular organization in mixed crystals that can modify centrosymmetric structure of pure material into acentric structure of host-guest compound. Such approach can help to alter organization of strongly polarized donoracceptor molecules in crystals and make them useful for applications as optoelectronic materials. In the mixed crystals of I and II organic components are benzene derivatives such as isomers of nitrotoluene, low-melting or liquid at room temperature. Crystal growth of these materials has been done using zone melting technique and molecular structure of these materials in pure compounds was compared with their structures in mixed crystals. It was found that number of acentric crystals in the series mixed crystals of I with nitrobenzene derivatives is higher than statistical expectation. Explanation of this phenomenon can be found in specific intermolecular interactions forming supramolecular associates in these materials.","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2008-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85352641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The solid solution Co3.6Mg1.4Cl2(TeO3)4 固溶体Co3.6Mg1.4Cl2(TeO3)4
Acta Crystallographica Pub Date : 2007-06-01 DOI: 10.1107/S1600536807024014
R. Takagi, D. Hjelmqvist, M. Johnsson
{"title":"The solid solution Co3.6Mg1.4Cl2(TeO3)4","authors":"R. Takagi, D. Hjelmqvist, M. Johnsson","doi":"10.1107/S1600536807024014","DOIUrl":"https://doi.org/10.1107/S1600536807024014","url":null,"abstract":"Complex transition metals oxyhalides containing a lone pair element, such as tellurium (IV), form an attractive research field because there is a high probability of finding new low-dimensionally arranged compounds and, particularly, a low-dimensionally arranged transition metals substructures, leading to interesting physical properties. Tellurium (IV) can drive the formation of many unusual structures because of its stereochemically active lone pair electrons, E. It commonly takes a coordination of three or four oxygen atoms to form either a TeO3E square pyramid or a TeO3+1E trigonal bipyramid. These lone pairs are very important players involved in lowering the dimensionality of crystal structures. Previous studies in transition metal tellurium (IV) oxohalide quarternary systems revealed a family of compounds, many of which exhibit interesting properties e.g. magnetic frustration. The unique point of this thesis is to employ alkaline earth elements (AE) to augment this ability of lone pair elements to lower the dimensionality of the transition metal arrangements. By this double usage of “chemical scissors” (a lone pair element used in conjunction with alkaline earth elements) we obtained new types of low-dimensionally arranged compounds.This thesis is focused on the syntheses and characterization of a series of compounds in the pentanary (five components) system AE-TeIV-TM-O-X (AE=alkaline earth metal, TM=transition metal and X=halogen), in which nine new compounds were found. The crystal structures of each of these compounds were determined by the single crystal X-ray diffraction data.","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"249 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2007-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73538306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
3-Amino-4H-pyrido[2,3-e]-1,2,4-thiadiazine 1,1-dioxide 3-Amino-4H-pyrido [2, 3 e) 1、2、1-dioxide 4-thiadiazine 1日
Acta Crystallographica Pub Date : 2001-07-01 DOI: 10.1107/S1600536801009904
L. Dupont, P. Tullio, S. Boverie, B. Pirotte
{"title":"3-Amino-4H-pyrido[2,3-e]-1,2,4-thiadiazine 1,1-dioxide","authors":"L. Dupont, P. Tullio, S. Boverie, B. Pirotte","doi":"10.1107/S1600536801009904","DOIUrl":"https://doi.org/10.1107/S1600536801009904","url":null,"abstract":"The title compound, C6H6N4O2S, was prepared for structural comparison with diazoxide (7-chloro-3-methyl-4H-1,2,4-benzo­thia­diazine 1,1-dioxide) and other 3-alkyl­amino­pyrido­thia­diazine 1,1-dioxides known to be potassium channel openers. Particular attention was paid to the tautomeric conformation adopted by the compound in the crystalline state, which is found to be the 4H-form.","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"98 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2001-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76107202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
a-Ammonium Vanadium Hydrogen Phosphate, a-NH4V(HPO4)2. a-磷酸氢钒铵，a-NH4V(HPO4)
Acta Crystallographica Pub Date : 1998-09-15 DOI: 10.1107/S0108270198002856
Z. Bircsak, W. Harrison
{"title":"a-Ammonium Vanadium Hydrogen Phosphate, a-NH4V(HPO4)2.","authors":"Z. Bircsak, W. Harrison","doi":"10.1107/S0108270198002856","DOIUrl":"https://doi.org/10.1107/S0108270198002856","url":null,"abstract":"α-Ammonium vanadium(III) bis(hydrogen phosphate) is a new ammonium vanadium(III) phosphate built up from a three-dimensional framework of VO6 octahedra and HPO4 tetrahedra [dav(V—O) = 2.008, dav(P—O) = 1.538, dav(N⋯O) = 3.086 A and θav(V—O—P) = 139.5°]. It is isostructural with α-RbV(HPO4)2 and complements the previously described β-NH4V(HPO4)2: α-NH4V(HPO4)2 contains both four-ring (two VO6 and two HPO4) and lantern (two VO6 and three HPO4) groupings, whereas β-NH4V(HPO4)2 contains only four-ring polyhedral groupings.","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"23 1","pages":"1195-1197"},"PeriodicalIF":0.0,"publicationDate":"1998-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79298136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Experimental Electron Density study of NaH2PO4 at 30 K NaH2PO4在30k下的实验电子密度研究
Acta Crystallographica Pub Date : 1998-02-01 DOI: 10.1107/S0108768197009622
M. Ichikawa, T. Gustafsson, I. Olovsson
{"title":"Experimental Electron Density study of NaH2PO4 at 30 K","authors":"M. Ichikawa, T. Gustafsson, I. Olovsson","doi":"10.1107/S0108768197009622","DOIUrl":"https://doi.org/10.1107/S0108768197009622","url":null,"abstract":"The deformation electron density of sodium dihydrogen phosphate, NaHzPO4, at 30 K has been studied as a reference for the electron-density characteristics of hydrogen-bonded ferroelectrics containing phosphate ions. Clear peaks of deformation electron density (0.30.6 e A -3) are seen in the middle of each P--O bond and electron deficiency (-0.2 to -0.4 e A -3) on the opposite side of each P--O bond peak. The peak height is higher and the peak shape is more distinct in P--O bonds than in P---O(H) bonds as a whole; the distribution of deformation density in the region of lone-pair electrons is more diffuse. The O--H...O bond deformationdensity peaks of around 0.2 e A -3 appear in the middle of the O--H bond, followed by a deeper electron depletion of around -0.4 e A -3 on the H...O contract, just outside the H atom. The effective charges, defined as the integral of the deformation electron density, have the following values: around +0.2 for Na, +1.8 for P, -0.8 for O and +0.6 for H. The correlation of the deformationdensity peaks and the depth of the negative peak of the H atom with the hydrogen-bond distance are discussed.","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"19 1","pages":"29"},"PeriodicalIF":0.0,"publicationDate":"1998-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80654206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Li+/Na+β-alumina: A Combined Single Crystal Neutron and X-ray Diffraction Study Li+/Na+β-氧化铝:单晶中子和x射线联合衍射研究
Acta Crystallographica Pub Date : 1997-08-01 DOI: 10.1107/S0108768197006629
K. Edström, T. Gustafsson, J. Thomas, G. Farrington
{"title":"Li+/Na+β-alumina: A Combined Single Crystal Neutron and X-ray Diffraction Study","authors":"K. Edström, T. Gustafsson, J. Thomas, G. Farrington","doi":"10.1107/S0108768197006629","DOIUrl":"https://doi.org/10.1107/S0108768197006629","url":null,"abstract":"The crystal structure and ionic distribution in the conduction plane of the partially exchanged Na+ beta-alumina system Li0.75Na0.47Al11O17.11 has been determined from single-crystal X-ray diffraction at 30 and 298 K, in combination with a single-crystal","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"23 1","pages":"631"},"PeriodicalIF":0.0,"publicationDate":"1997-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87100410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Quantum chemical and experimental study of urea 尿素的量子化学及实验研究
Acta Crystallographica Pub Date : 1996-08-08 DOI: 10.1107/S0108767396085455
D. Feil, R. D. Vries, V. Tsirelson, V. Zavodnik
{"title":"Quantum chemical and experimental study of urea","authors":"D. Feil, R. D. Vries, V. Tsirelson, V. Zavodnik","doi":"10.1107/S0108767396085455","DOIUrl":"https://doi.org/10.1107/S0108767396085455","url":null,"abstract":"","PeriodicalId":7001,"journal":{"name":"Acta Crystallographica","volume":"554 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"1996-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89208139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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