Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms
- PMID: 27288866
- DOI: 10.1016/j.jsb.2016.06.005
Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms
Abstract
Cryo electron tomography allows macromolecular complexes within vitrified, intact, thin cells or sections thereof to be visualized, and structural analysis to be performed in situ by averaging over multiple copies of the same molecules. Image processing for subtomogram averaging is specific and cumbersome, due to the large amount of data and its three dimensional nature and anisotropic resolution. Here, we streamline data processing for subtomogram averaging by introducing an archiving system, Dynamo Catalogue. This system manages tomographic data from multiple tomograms and allows visual feedback during all processing steps, including particle picking, extraction, alignment and classification. The file structure of a processing project file structure includes logfiles of performed operations, and can be backed up and shared between users. Command line commands, database queries and a set of GUIs give the user versatile control over the process. Here, we introduce a set of geometric tools that streamline particle picking from simple (filaments, spheres, tubes, vesicles) and complex geometries (arbitrary 2D surfaces, rare instances on proteins with geometric restrictions, and 2D and 3D crystals). Advanced functionality, such as manual alignment and subboxing, is useful when initial templates are generated for alignment and for project customization. Dynamo Catalogue is part of the open source package Dynamo and includes tools to ensure format compatibility with the subtomogram averaging functionalities of other packages, such as Jsubtomo, PyTom, PEET, EMAN2, XMIPP and Relion.
Keywords: Cryo electron tomography; Data management; Subtomogram averaging.
Copyright © 2016. Published by Elsevier Inc.
Similar articles
-
Cryo-Electron Tomography and Subtomogram Averaging.Methods Enzymol. 2016;579:329-67. doi: 10.1016/bs.mie.2016.04.014. Epub 2016 Jun 22. Methods Enzymol. 2016. PMID: 27572733 Review.
-
Subtomogram averaging from cryo-electron tomograms.Methods Cell Biol. 2019;152:217-259. doi: 10.1016/bs.mcb.2019.04.003. Epub 2019 May 15. Methods Cell Biol. 2019. PMID: 31326022 Review.
-
PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis.J Struct Biol. 2012 May;178(2):177-88. doi: 10.1016/j.jsb.2011.12.003. Epub 2011 Dec 13. J Struct Biol. 2012. PMID: 22193517
-
Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION.Nat Protoc. 2016 Nov;11(11):2054-65. doi: 10.1038/nprot.2016.124. Epub 2016 Sep 29. Nat Protoc. 2016. PMID: 27685097 Free PMC article.
-
Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.J Struct Biol. 2012 May;178(2):139-51. doi: 10.1016/j.jsb.2011.12.017. Epub 2012 Jan 8. J Struct Biol. 2012. PMID: 22245546
Cited by
-
Membrane-assisted assembly and selective secretory autophagy of enteroviruses.Nat Commun. 2022 Oct 10;13(1):5986. doi: 10.1038/s41467-022-33483-7. Nat Commun. 2022. PMID: 36216808 Free PMC article.
-
Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM.Nat Commun. 2020 Jul 24;11(1):3709. doi: 10.1038/s41467-020-17466-0. Nat Commun. 2020. PMID: 32709843 Free PMC article.
-
Cerebral Corpora amylacea are dense membranous labyrinths containing structurally preserved cell organelles.Sci Rep. 2018 Dec 21;8(1):18046. doi: 10.1038/s41598-018-36223-4. Sci Rep. 2018. PMID: 30575769 Free PMC article.
-
Strategies for picking membrane-associated particles within subtomogram averaging workflows.Faraday Discuss. 2022 Nov 8;240(0):101-113. doi: 10.1039/d2fd00022a. Faraday Discuss. 2022. PMID: 35924570 Free PMC article.
-
The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins.Nat Commun. 2019 Feb 19;10(1):846. doi: 10.1038/s41467-019-08728-7. Nat Commun. 2019. PMID: 30783086 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources