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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]]. | 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 = | = Cite = | ||
Please cite these papers if ''Dynamo'' is useful in your research: | 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/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 | * [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 | ||
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* [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://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. | ||
Latest revision as of 12:59, 1 August 2024
Dynamo is a software environment for subtomogram averaging of cryo-EM data.
This wiki guides new Dynamo users all the way from tomograms to averages and classes. In a full workflow, you would organize tomograms in catalogues, use them to pick particles and create alignment and classification projects to be run on different computing environments.
Participate
There is a [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:
- 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.
- 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
- 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).
- 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.
- 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.
- Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo., Coray et al. Structure, July 2024.
