Automatic modeling methods using cryoelectron microscopy (cryoEM) density maps as constraints are promising approaches to building atomic models of individual proteins or protein domains. However, their application to large macromolecular assemblies has not been possible largely due to computational limitations inherent to such unsupervised methods. Here we describe a new method, EM-IMO (electron microscopy-iterative modular optimization), for building, modifying and refining local structures of protein models using cryoEM maps as a constraint. As a supervised refinement method, EM-IMO allows users to specify parameters derived from inspections so as to guide, and as a consequence, significantly speed up the refinement. An EM-IMO-based refinement protocol is first benchmarked on a data set of 50 homology models using simulated density maps. A multiscale refinement strategy that combines EM-IMO-based and molecular dynamics-based refinement is then applied to build backbone models for the seven conformers of the five capsid proteins in our near-atomic-resolution cryoEM map of the grass carp reovirus virion, a member of the Aquareovirus genus of the Reoviridae family. The refined models allow us to reconstruct a backbone model of the entire grass carp reovirus capsid and provide valuable functional insights that are described in the accompanying publication [Cheng, L., Zhu, J., Hui, W. H., Zhang, X., Honig, B., Fang, Q. & Zhou, Z. H. (2010). Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics. J. Mol. Biol. (this issue). doi:10.1016/j.jmb.2009.12.027.]. Our study demonstrates that the integrated use of homology modeling and a multiscale refinement protocol that combines supervised and automated structure refinement offers a practical strategy for building atomic models based on medium- to high-resolution cryoEM density maps.