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Journal of Applied Crystallography最新文献

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crystchemlib: a Python library and GUI for analysis of crystal structure datasets
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2025-01-24 DOI: 10.1107/S1600576724011956
Sergey V. Rashchenko
{"title":"crystchemlib: a Python library and GUI for analysis of crystal structure datasets","authors":"Sergey V. Rashchenko","doi":"10.1107/S1600576724011956","DOIUrl":"https://doi.org/10.1107/S1600576724011956","url":null,"abstract":"<p>The problem of extracting basic (<i>e.g.</i> bond lengths and angles) and advanced (<i>e.g.</i> polyhedron volumes and effective coordination numbers) crystal chemical parameters from large datasets of CIFs in a quick and flexible way is addressed by a lightweight Python library with a graphical user interface (GUI). A description of library functionality in the GUI and scripting modes followed by examples based on open-access data demonstrate its advantages for crystallographers working with pressure-, temperature- and chemistry-induced structural variations, as well as with analysis of structural databases.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"290-295"},"PeriodicalIF":5.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253049","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}
引用次数: 0
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-24
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"96-106"},"PeriodicalIF":5.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253178","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}
引用次数: 0
Calculation of pair distribution functions from small-angle X-ray scattering protein data by direct transform
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-24 DOI: 10.1107/S1600576724011695
John Badger
{"title":"Calculation of pair distribution functions from small-angle X-ray scattering protein data by direct transform","authors":"John Badger","doi":"10.1107/S1600576724011695","DOIUrl":"https://doi.org/10.1107/S1600576724011695","url":null,"abstract":"<p>In a small-angle X-ray scattering analysis of protein molecules in solution the calculation of the pair distribution function, <i>P</i>(<i>r</i>), is invariably performed by an indirect Fourier transform. This approach models a <i>P</i>(<i>r</i>) to fit the available intensity data, <i>I</i>(<i>q</i>). The determination of <i>P</i>(<i>r</i>) via a direct transform from <i>I</i>(<i>q</i>) has been dismissed as unworkable since the range of <i>q</i> that is experimentally measured is necessarily incomplete. Here, it is shown that, provided suitable measures are taken to estimate unmeasured low-resolution data and avoid a sharp data truncation at the high-resolution data limit, the appearance of significant artifacts in the resulting <i>P</i>(<i>r</i>) may be circumvented. Using several examples taken from the Small Angle Scattering Biological Data Bank, it is demonstrated that the <i>P</i>(<i>r</i>) obtained by a direct transform are in close agreement with the <i>P</i>(<i>r</i>) obtained using the popular indirect transform program <i>GNOM</i>.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"119-127"},"PeriodicalIF":5.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253180","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}
引用次数: 0
ASUGNN: an asymmetric-unit-based graph neural network for crystal property prediction
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-24 DOI: 10.1107/S1600576724011336
Barnie Cao, Daniel Anderson, Luke Davis
{"title":"ASUGNN: an asymmetric-unit-based graph neural network for crystal property prediction","authors":"Barnie Cao,&nbsp;Daniel Anderson,&nbsp;Luke Davis","doi":"10.1107/S1600576724011336","DOIUrl":"https://doi.org/10.1107/S1600576724011336","url":null,"abstract":"<p>Material properties can often be derived directly from fundamental equations governing electron behavior. In this study, we present an open-source asymmetric-unit-based graph neural network designed to capture atomic patterns and their corresponding electron distributions. By coarse-graining sites belonging to conjugate subgroups and analyzing reciprocal space through powder X-ray diffraction patterns, our model predicts key physical properties, including formation energy, band gap, bulk modulus and metal/non-metal classification. Our method demonstrates exceptional predictive accuracy for properties calculated using density functional theory across the Materials Project dataset. Our approach is compared with state-of-the-art models and exhibits impressively low error rates in zero-shot predictions.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"87-95"},"PeriodicalIF":5.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253182","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}
引用次数: 0
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-24
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"107-118"},"PeriodicalIF":5.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253181","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}
引用次数: 0
Integrating fundamental concepts with practical skills: consolidating small-molecule crystallography education
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-24 DOI: 10.1107/S1600576724011373
Shao-Liang Zheng, Nicholas P. Litak, Michael G. Campbell, Rex C. Handford, Dilek K. Dogutan, Kurtis M. Carsch, Theodore A. Betley
{"title":"Integrating fundamental concepts with practical skills: consolidating small-molecule crystallography education","authors":"Shao-Liang Zheng,&nbsp;Nicholas P. Litak,&nbsp;Michael G. Campbell,&nbsp;Rex C. Handford,&nbsp;Dilek K. Dogutan,&nbsp;Kurtis M. Carsch,&nbsp;Theodore A. Betley","doi":"10.1107/S1600576724011373","DOIUrl":"https://doi.org/10.1107/S1600576724011373","url":null,"abstract":"<p>A comprehensive educational strategy designed to make small-molecule crystallography more accessible for students at various academic levels is described. By integrating hands-on laboratory visits, structured courses and advanced application training, we cultivate a deep understanding of fundamental crystallographic concepts while fostering practical skills. This strategy also aims to inspire novice learners, building their confidence and interest in structural science. Our approach demystifies complex concepts through real-world examples and interactive case-learning modules, enabling students to proficiently apply crystallography in their research. The resulting educational impact is evident in numerous publications from undergraduates, scholarship awards to graduates and successful independent research projects, highlighting the effectiveness of our programme in inspiring the next generation of chemical crystallographers.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"269-275"},"PeriodicalIF":5.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253177","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}
引用次数: 0
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-24
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"76-86"},"PeriodicalIF":5.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143253183","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}
引用次数: 0
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-17
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"4-17"},"PeriodicalIF":5.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143252858","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}
引用次数: 0
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-17
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"71-75"},"PeriodicalIF":5.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143252860","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}
引用次数: 0
High-accuracy high-resolution measurements of fluorescence in manganese using extended-range high-energy-resolution fluorescence detection
IF 5.2 3区 材料科学
Journal of Applied Crystallography Pub Date : 2024-12-17 DOI: 10.1107/S1600576724010574
Daniel Sier, Nicholas T. T. Tran, Tony Kirk, Chanh Q. Tran, J. Frederick W. Mosselmans, Sofia Diaz-Moreno, Christopher T. Chantler
{"title":"High-accuracy high-resolution measurements of fluorescence in manganese using extended-range high-energy-resolution fluorescence detection","authors":"Daniel Sier,&nbsp;Nicholas T. T. Tran,&nbsp;Tony Kirk,&nbsp;Chanh Q. Tran,&nbsp;J. Frederick W. Mosselmans,&nbsp;Sofia Diaz-Moreno,&nbsp;Christopher T. Chantler","doi":"10.1107/S1600576724010574","DOIUrl":"https://doi.org/10.1107/S1600576724010574","url":null,"abstract":"<p>The technique of extended-range high-energy-resolution fluorescence detection (XR-HERFD), developed from X-ray absorption spectroscopy, X-ray emission spectroscopy and resonant inelastic X-ray scattering (RIXS), has been used to successfully observe a new X-ray fluorescent satellite in manganese. The experimental methodology, spectral processing and analysis, and how statistical information and structure can be defined, extracted and used from HERFD spectra are detailed. Novel approaches to measure and improve accurate data uncertainty in XR-HERFD, HERFD and RIXS data sets are also presented. This includes definitions of intrinsic resolution and improvements to the resolution of the output and data by a factor of two relative to raw data or standard processing. Novel systematics common in HERFD and RIXS experiments are detailed, including background subtraction and elastic Bragg harmonics, with approaches to dealing with them.</p>","PeriodicalId":48737,"journal":{"name":"Journal of Applied Crystallography","volume":"58 1","pages":"42-59"},"PeriodicalIF":5.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143252861","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}
引用次数: 0
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