title: Hybrid Electron Microscopy Normal Mode Analysis graphical interface and protocol.
abstract: This article presents an integral graphical interface to the Hybrid Electron Microscopy Normal Mode Analysis (HEMNMA) approach that was developed for capturing continuous motions of large macromolecular complexes from single-particle EM images. HEMNMA was shown to be a good approach to analyze multiple conformations of a macromolecular complex but it could not be widely used in the EM field due to a lack of an integral interface. In particular, its use required switching among different software sources as well as selecting modes for image analysis was difficult without the graphical interface. The graphical interface was thus developed to simplify the practical use of HEMNMA. It is implemented in the open-source software package Xmipp 3.1 (http://xmipp.cnb.csic.es) and only a small part of it relies on MATLAB that is accessible through the main interface. Such integration provides the user with an easy way to perform the analysis of macromolecular dynamics and forms a direct connection to the single-particle reconstruction process. A step-by-step HEMNMA protocol with the graphical interface is given in full details in Supplementary material. The graphical interface will be useful to experimentalists who are interested in studies of continuous conformational changes of macromolecular complexes beyond the modeling of continuous heterogeneity in single particle reconstruction.
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología - CSIC, 28049 Madrid, Spain.
authors.forename: Carlos Oscar S
authors.initials: CO
authors.lastname: Sorzano
authors.affiliation: Biocomputing Unit, Centro Nacional de Biotecnología - CSIC, 28049 Madrid, Spain.
authors.forename: José Miguel
authors.initials: JM
authors.lastname: de la Rosa-Trevín
authors.affiliation: RIKEN, Advanced Institute for Computational Sciences, Kobe, Hyogo 650-0047, Japan.
authors.forename: Florence
authors.initials: F
authors.lastname: Tama
authors.affiliation: IMPMC, Sorbonne Universités - CNRS UMR 7590, UPMC Univ Paris 6, MNHN, IRD UMR 206, 75005 Paris, France. Electronic address: Slavica.Jonic@impmc.upmc.fr.
authors.forename: Slavica
authors.initials: S
authors.lastname: Jonić
mesh_terms: D000465:Algorithms; D007091:Image Processing, Computer-Assisted / Q000379:methods; D021621:Imaging, Three-Dimensional / Q000379:methods; D046911:Macromolecular Substances / Q000737:chemistry*; D008854:Microscopy, Electron / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D046911:Macromolecular Substances
keywords: Continuous conformational changes; Dynamics; Normal Mode Analysis; Single particle analysis; Software; Structure