Dynamo wiki_dynamo_biozentrum_unibas_01 https://www.dynamo-em.org//w/index.php?title=Main_Page MediaWiki 1.34.0 first-letter Media Special Talk User User talk Dynamo Dynamo talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 1 5633 5624 2025-09-12T09:18:32Z Raffaele Coray 6 wikitext text/x-wiki {{DISPLAYTITLE:''Dynamo''}} ''Dynamo'' is a software environment for subtomogram averaging of cryo-EM data. This wiki [[Getting started|guides new ''Dynamo'' users]] all the way from tomograms to averages and classes. In a full workflow, you would organize tomograms in [[Catalogue | catalogues]], use them to [[Particle picking|pick particles]] and create [[Subtomogram alignment|alignment]] and [[Classification |classification projects]] to be run on different [[computing environments]]. = Participate = There is a [[https://groups.google.com/forum/#!forum/dynamo-for-cryo-electron-tomography forum in Google Groups]] where you can present your questions to developers and other users. Bear in mind that you need a Google account for this. = Cite = Please cite these papers if ''Dynamo'' is useful in your research: * [http://www.sciencedirect.com/science/article/pii/S1047847711003650|''Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.''] Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H., J. Struct. Biol. 2012. * [http://www.sciencedirect.com/science/article/pii/S1047847716301113| ''Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms''] Castaño-Díez D, Kudryashev M, Stahlberg H., in J Struct Biol. 2017 Feb; 197(2):135-144 * [https://doi.org/10.1107/S2059798317003369''The Dynamo package for tomography and subtomogram averaging: components for MATLAB, GPU computing and EC2 Amazon Web Services''] Castaño-Díez D. in Acta Crystallographica Section D: Structural Biology 73 (6). * [https://doi.org/10.3389/fmolb.2018.00082''Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package''] Navarro PP, Stahlberg H and Castaño-Díez D (2018). Front. Mol. Biosci. 5:82. * [https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001318''Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo''] Scaramuzza S, Castaño-Díez D (2021). PLoS biology. 19(8):e3001318. * [https://doi.org/10.1016/j.str.2024.07.003 ''Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo.''], Coray et al. Structure, July 2024. * [https://doi.org/10.1016/j.str.2025.06.009 ''Geometry-aware template matching for cryo-electron tomograms in Dynamo.''], Coray et al. Structure, September 2025. = Founding Agencies = [[File:AE_logo.jpg|170px|left]] [[File: Snf_logo_rgb_standard_en_pos.png |400px|right]] [[File: Logo_hfsp.jpg |400px|center]] 0migenhb5kponwx0qohiwan4r8n0yvc