title: Methods to account for movement and flexibility in cryo-EM data processing.
abstract: Recent advances in direct electron detectors and improved CMOS cameras have been accompanied by the development of a range of software to take advantage of the data they produce. In particular they allow for the correction of two types of motion in cryo electron microscopy samples: motion correction for movements of the sample particles in the ice, and differential masking to account for heterogeneity caused by flexibility within protein complexes. Here we provide several scripts that allow users to move between RELION and standalone motion correction and centring programs. We then compare the computational cost and improvements in data quality with each program. We also describe our masking procedures to account for conformational flexibility. For the different elements of this study we have used three samples; a high symmetry virus, flexible protein complex (∼1MDa) and a relatively small protein complex (∼550kDa), to benchmark four widely available motion correction packages. Using these as test cases we demonstrate how motion correction and differential masking, as well as an additional particle re-centring protocol can improve final reconstructions when used within the RELION image-processing package.
authors.affiliation: School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: S
authors.initials: S
authors.lastname: Rawson
authors.affiliation: School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: M G
authors.initials: MG
authors.lastname: Iadanza
authors.affiliation: School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
authors.forename: N A
authors.initials: NA
authors.lastname: Ranson
authors.affiliation: School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. Electronic address: s.p.muench@leeds.ac.uk.
authors.forename: S P
authors.initials: SP
authors.lastname: Muench
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D020285:Cryoelectron Microscopy / Q000379:methods; D007091:Image Processing, Computer-Assisted; D046911:Macromolecular Substances / Q000737:chemistry / Q000648:ultrastructure; D008958:Models, Molecular; D012984:Software
chemical_list: D046911:Macromolecular Substances
keywords: Cryo-EM; Image processing; Motion correction; RELION