The methods and applications that integrate electron microscopic density maps and comparative atomic coordinates to generate atomic models of protein complexes and their assemblies have recently advanced. Here, we also report on a newly developed tool for integration between density maps at a spatial resolution of about one nanometer and atomic coordinates by introducing the spatial constraints into a molecular dynamics calculation, which we call spatially restricted molecular dynamics. We, successfully, constructed the atomic models well-fitted to the density maps generated from nine different atomic coordinates of proteins. The method will give us the useful, refined, and presumable atomic structure of macromolecules to elucidate the relationship between their structure and functions.