eb782c3cbd923830426e4a5fe4af5895 pmc_34684805.pdf 4eded29a846c29fe01923142c8d80364e8c635e4 pmc_34684805.pdf 6c79e3635577367fc829eb85720fa33abe58a78c2e9ee1b5f1057bff78ef910a pmc_34684805.pdf Title: Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion Subject: Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package. Keywords: Xmipp; Cryo-EM; Scipion; single-particle analysis Author: David Strelak, Amaya Jiménez-Moreno, José L. Vilas, Erney Ramírez-Aportela, Ruben Sánchez-García, David Maluenda, Javier Vargas, David Herreros, Estrella Fernández-Giménez, Federico P. de Isidro-Gómez, Jan Horacek, David Myska, Martin Horacek, Pablo Conesa, Yunior C. Fonseca-Reyna, Jorge Jiménez, Marta Martínez, Mohamad Harastani, Slavica Jonić, Jiri Filipovic, Roberto Marabini, José M. Carazo and Carlos O. S. Sorzano Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Fri Oct 15 09:20:48 2021 CEST ModDate: Fri Oct 15 09:36:58 2021 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 14 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 431465 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- WQFSCO+URWPalladioL-Ital Type 1 Custom yes yes no 10 0 KBFBTB+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 DWCXYS+URWPalladioL-Roma Type 1 Custom yes yes no 19 0 PUSVWS+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 27 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 49 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 53 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 57 0 GRVGLX+SFTT1000 Type 1 Custom yes yes no 70 0 CRJHCU+PazoMath-Italic Type 1 Builtin yes yes no 92 0 BCYCBW+LiberationSans TrueType WinAnsi yes yes yes 102 0 HJTPKX+LiberationSans TrueType WinAnsi yes yes yes 110 0 HJTPKX+LiberationSans TrueType WinAnsi yes yes yes 118 0 SZAUZU+LiberationSans TrueType WinAnsi yes yes yes 130 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2022-03-22 02:38:56 CET RepresentationInformation: pmc_34684805.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2022-01-10 08:29:17 CET Size: 431465 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 417 FreeObjects: 9 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: New Programs and Protocols Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Children: Item: Title: Movie Acquisition and Frame Alignment Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: CTF Estimation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: Particle Picking Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: 2D Classification Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Ab-Initio Model Building Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: 3D Alignment and Reconstruction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: 3D Classification Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Sharpening, Denoising, and (Local) Resolution Estimation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Model Building Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Our Other Contributions and Xmipp Applications Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: GPU Acceleration Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: New Programs and Protocols Summary Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Technologies Used in Xmipp Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Summary Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Info: Title: Advances in Xmipp for Cryo Electron Microscopy: From Xmipp to Scipion Author: いちぶどつ〠こぴひづぬちに〬〠ぁねちべち〠おどねラのづぺ〭きはひづのは〬〠おはびラ〠が〮〠ざどぬちび〬〠ぅひのづべ〠げちねロひづぺ〭ぁばはひぴづぬち〬〠げふぢづの〠こメのっとづぺ〭ぇちひっロち〬〠いちぶどつ〠きちぬふづのつち〬〠おちぶどづひ〠ざちひでちび〬〠いちぶどつ〠えづひひづひはび〬〠ぅびぴひづぬぬち〠うづひのメのつづぺ〭ぇどねラのづぺ〬〠うづつづひどっは〠ぐ〮〠つづ〠ぉびどつひは〭ぇンねづぺ〬〠おちの〠えはひちっづに〬〠いちぶどつ〠きべびにち〬〠きちひぴどの〠えはひちっづに〬〠ぐちぢぬは〠ぃはのづびち〬〠すふのどはひ〠ぃ〮〠うはのびづっち〭げづべのち〬〠おはひでづ〠おどねラのづぺ〬〠きちひぴち〠きちひぴロのづぺ〬〠きはとちねちつ〠えちひちびぴちのど〬〠こぬちぶどっち〠おはのどㅜ〰㝜〰〬〠おどひど〠うどぬどばはぶどっ〬〠げはぢづひぴは〠きちひちぢどのど〬〠おはびラ〠き〮〠ぃちひちぺは〠ちのつ〠ぃちひぬはび〠く〮〠こ〮〠こはひぺちのは Subject: Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package. Keywords: Xmipp; Cryo-EM; Scipion; single-particle analysis Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Fri Oct 15 09:20:48 CEST 2021 ModDate: Fri Oct 15 09:36:58 CEST 2021 ID: 0xe2f20963ada118077be036149614048b, 0xe2f20963ada118077be036149614048b Filters: FilterPipeline: FlateDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 1241 ImageHeight: 857 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Fonts: Type1: Font: BaseFont: DWCXYS+URWPalladioL-Roma FontSubset: true FirstChar: 2 LastChar: 253 FontDescriptor: FontName: DWCXYS+URWPalladioL-Roma Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: GRVGLX+SFTT1000 FontSubset: true FirstChar: 40 LastChar: 124 FontDescriptor: FontName: GRVGLX+SFTT1000 Flags: Symbolic FontBBox: -208, -360, 1374, 838 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: WQFSCO+URWPalladioL-Ital 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