title: High resolution single particle refinement in EMAN2.1.
abstract: EMAN2.1 is a complete image processing suite for quantitative analysis of grayscale images, with a primary focus on transmission electron microscopy, with complete workflows for performing high resolution single particle reconstruction, 2-D and 3-D heterogeneity analysis, random conical tilt reconstruction and subtomogram averaging, among other tasks. In this manuscript we provide the first detailed description of the high resolution single particle analysis pipeline and the philosophy behind its approach to the reconstruction problem. High resolution refinement is a fully automated process, and involves an advanced set of heuristics to select optimal algorithms for each specific refinement task. A gold standard FSC is produced automatically as part of refinement, providing a robust resolution estimate for the final map, and this is used to optimally filter the final CTF phase and amplitude corrected structure. Additional methods are in-place to reduce model bias during refinement, and to permit cross-validation using other computational methods.
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Bell
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Muyuan
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Psychiatry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Philip R
authors.initials: PR
authors.lastname: Baldwin
authors.affiliation: Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA. Electronic address: sludtke@bcm.edu.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Ludtke
mesh_terms: D000465:Algorithms; D020285:Cryoelectron Microscopy; D021621:Imaging, Three-Dimensional; D046529:Microscopy, Electron, Transmission; D008958:Models, Molecular; D025341:Principal Component Analysis; D012984:Software
keywords: 3-D reconstruction; CryoEM; Image processing; Single particle analysis; Structural biology