Journal of Applied Crystallography最新文献

{"title":"Powder-diffraction-based structural comparison for crystal structure prediction without prior indexing","authors":"Alberto Otero-de-la-Roza","doi":"10.1107/S1600576724007489","DOIUrl":"https://doi.org/10.1107/S1600576724007489","url":null,"abstract":"<p>The objective of crystal structure prediction (CSP) is to predict computationally the thermodynamically stable crystal structure of a compound from its stoichiometry or its molecular diagram. Crystal similarity indices measure the degree of similarity between two crystal structures and are essential in CSP because they are used to identify duplicates. Powder-based indices, which are based on comparing X-ray diffraction patterns, allow the use of experimental X-ray powder diffraction data to inform the CSP search. Powder-assisted CSP presents two unique difficulties: (i) the experimental and computational structures are not entirely comparable because the former is subject to thermal expansion from lattice vibrations, and (ii) experimental patterns present features (noise, background contribution, varying peak shapes <i>etc.</i>) that are not easily predictable computationally. This work presents a powder-based similarity index (GPWDF) based on a modification of the index introduced by de Gelder, Wehrens &amp; Hageman [<i>J. Comput. Chem.</i> (2001), <b>22</b>, 273–289] using cross-correlation functions that can be calculated analytically. Based on GPWDF, a variable-cell similarity index (VC-GPWDF) is also proposed that assigns a high similarity score to structures that differ only by a lattice deformation and which takes advantage of the analytical derivatives of GPWDF with respect to the lattice parameters. VC-GPWDF can be used to identify similarity between two computational structures generated using different methods, between a computational and an experimental structure, and between two experimental structures measured under different conditions (<i>e.g.</i> different temperature and pressure). VC-GPWDF can also be used to compare crystal structures with experimental patterns in combination with an automatic pre-processing step. The proposed similarity indices are simple, efficient and fully automatic. They do not require indexing of the experimental pattern or a guess of the space group, they account for deformations caused by varying experimental conditions, they give meaningful results even when the experimental pattern is of very poor quality, and their computational cost does not increase with the flexibility of the molecular motif.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting the ‘magic condition’ on the basis of the Takagi–Taupin theory","authors":"Yu-Hang Wang,&nbsp;Ming Li,&nbsp;Le Kang,&nbsp;Quan-Jie Jia","doi":"10.1107/S1600576724006903","DOIUrl":"https://doi.org/10.1107/S1600576724006903","url":null,"abstract":"<p>A numerical framework based on the integral solution of the Takagi–Taupin equations has been developed for cylindrically bent Laue crystals. On the basis of this framework, diffraction geometries that satisfy the `magic condition' have been studied from the perspective of dynamical theory. The numerical findings indicate that, in certain diffraction geometries, the focusing behaviour of cylindrically bent Laue crystals will be notably influenced by dynamical effects and the foci of different energies will not converge as predicted by the `magic condition', which is derived from geometric optics theory. These dynamical effects are further explained through a direct numerical analysis of the influence function.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of specimen displacement in X-ray powder diffraction measurements with laboratory diffractometers","authors":"M. Gateshki,&nbsp;Th. Dortmann,&nbsp;Th. Degen,&nbsp;M. Sadki,&nbsp;N. Norberg","doi":"10.1107/S1600576724006460","DOIUrl":"https://doi.org/10.1107/S1600576724006460","url":null,"abstract":"<p>The effect of specimen displacement in X-ray powder diffraction experiments with laboratory diffractometers has been revisited and new expressions have been derived for several commonly used experimental configurations, including Bragg–Brentano parafocusing geometry and flat-plate transmission geometry. The results presented in this work allow the analysis of data from samples with relatively large displacements. This may open the possibility to study samples with dimensions that are difficult to accommodate with the sample-handling capabilities of standard laboratory diffractometers.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MIPDS: a comprehensive database on the molecular interactions in protein dimer structures","authors":"Madhumathi Sanjeevi,&nbsp;Santhosh Rajendran,&nbsp;Jeyakanthan Jeyaraman,&nbsp;Kanagaraj Sekar","doi":"10.1107/S1600576724007131","DOIUrl":"https://doi.org/10.1107/S1600576724007131","url":null,"abstract":"<p>Although many studies have addressed the significance of interactions in the dimeric structures of proteins, there is no dedicated database of these interactions. To this end, the Molecular Interactions in Protein Dimer Structure (MIPDS) database has been developed; it is an open-access repository containing 60 298 3D structures of dimeric proteins sourced from the Protein Data Bank. This helps researchers comprehend the types of interaction, which include those mediated by water, small molecules or ligands and direct interactions, in 3D structures at the molecular level. The database is accessible through a user-friendly interface, where users can conduct searches based on PDB accession number, interaction type and geometric parameters. It can be viewed in textual and graphical formats using the plug-in <i>JSmol</i>. MIPDS is updated weekly using programmed scripts to incorporate newly released dimeric structures and analyses of their interaction types. The database is intended for the scientific community working in structural biology, structural bioinformatics, drug discovery and development. MIPDS is freely accessible to users worldwide at http://dicsoft1.physics.iisc.ac.in/mipds.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":5.2,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142430121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}