Transmembrane (TM) proteins that form alpha-helix bundles constitute approximately 50% of contemporary drug targets. Yet, it is difficult to determine their high-resolution (< 4 A) structures. Some TM proteins yield more easily to structure determination using cryo electron microscopy (cryo-EM), though this technique most often results in lower resolution structures, precluding an unambiguous assignment of TM amino acid sequences to the helices seen in the structure. We present computational tools for assigning the TM segments in the proteins sequence to the helices seen in cryo-EM structures.