Abstract-Experimental structure analysis of biological molecules (e.g, proteins) or macromolecular complexes (e.g, viruses) can be used to generate three-dimensional density maps of these entities. Such a density map can be viewed as a three-dimensional gray-scale image where space is subdivided in voxels of a given size. The focus of this paper is the analysis of virus density maps. The hull of a virus consists of many copies of one or several different proteins. An important tool for the study of viruses is cryo-electron microscopy (cryo-EM), a technique with insufficient resolution to directly determine the arrangement of the proteins in the virus. We therefore created a tool that locates proteins in the three-dimensional density map of a virus. The goal is to fully determine the locations and orientations of the protein(s) in the virus given the virus' three-dimensional density map and a database of density maps of one or more protein candidates.