We report here the protocol adopted to build the atomic model of the newly discovered virus FLiP (Elavobacterium infecting, lipid-containing phage) into 3.9 angstrom cryo-electron microscopy (cryo-EM) maps. In particular, this report discusses the combination of density modification procedures, automatic model building and bioinformatics tools applied to guide the tracing of the major capsid protein (MCP) of this virus. The protocol outlined here may serve as a reference for future structural determination by cryo-EM of viruses lacking detectable structural homologues.