title: A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.
abstract: Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a "toolbox" of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map.
authors.affiliation: National Resource for Automated Molecular Microscopy and Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Neil R
authors.initials: NR
authors.lastname: Voss
authors.forename: Dmitry
authors.initials: D
authors.lastname: Lyumkis
authors.forename: Anchi
authors.initials: A
authors.lastname: Cheng
authors.forename: Pick-Wei
authors.initials: PW
authors.lastname: Lau
authors.forename: Anke
authors.initials: A
authors.lastname: Mulder
authors.forename: Gabriel C
authors.initials: GC
authors.lastname: Lander
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Brignole
authors.forename: Denis
authors.initials: D
authors.lastname: Fellmann
authors.forename: Christopher
authors.initials: C
authors.lastname: Irving
authors.forename: Erica L
authors.initials: EL
authors.lastname: Jacovetty
authors.forename: Albert
authors.initials: A
authors.lastname: Leung
authors.forename: James
authors.initials: J
authors.lastname: Pulokas
authors.forename: Joel D
authors.initials: JD
authors.lastname: Quispe
authors.forename: Hanspeter
authors.initials: H
authors.lastname: Winkler
authors.forename: Craig
authors.initials: C
authors.lastname: Yoshioka
authors.forename: Bridget
authors.initials: B
authors.lastname: Carragher
authors.forename: Clinton S
authors.initials: CS
authors.lastname: Potter
mesh_terms: D000465:Algorithms; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D046529:Microscopy, Electron, Transmission / Q000379:methods*; D054681:Ribosome Subunits, Large, Bacterial / Q000648:ultrastructure; D012984:Software