title: Real-space processing of helical filaments in SPARX.
abstract: We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional features include a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy.
authors.affiliation: Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, Otto-Hahn-Straße 11, 44227 Dortmund, Germany.
authors.forename: Elmar
authors.initials: E
authors.lastname: Behrmann
authors.forename: Guozhi
authors.initials: G
authors.lastname: Tao
authors.forename: David L
authors.initials: DL
authors.lastname: Stokes
authors.forename: Edward H
authors.initials: EH
authors.lastname: Egelman
authors.forename: Stefan
authors.initials: S
authors.lastname: Raunser
authors.forename: Pawel A
authors.initials: PA
authors.lastname: Penczek
mesh_terms: D008841:Actin Cytoskeleton / Q000737:chemistry; D000205:Actomyosin / Q000737:chemistry*; D000465:Algorithms; D020285:Cryoelectron Microscopy / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008958:Models, Molecular; D025341:Principal Component Analysis; D020836:Protein Structure, Quaternary; D012984:Software
chemical_list: D000205:Actomyosin