Rigid-Body Fitting of Atomic Models on 3D Density Maps of Electron Microscopy

Cryo electron microscopy has revolutionarily evolved for the determination of the 3D structure of macromolecular complexes. The modeling procedures on the 3D density maps of electron microscopy are roughly classified into three categories: fitting, de novo modeling and refinement. The registered atomic models from the maps have mostly been hand-built and auto-refined. Several programs aiming at automatic modeling have also been developed using various kinds of molecular representations. Among these three classes of the modeling procedures, the rigid body fitting is reviewed here, because it is the most basic modeling process applied before the other steps. The fitting problems are classified as the fittings of single subunit or multiple subunits, and the fittings on global or local parts of maps. A higher resolution map enables more local fitting. Various molecular representations have been employed in the fitting programs. A point and digital image models are generally used to represent molecules, but new representations, such as the Gaussian mixture model, have been applied recently.