Hello, I was hoping you could help me out. I am trying to locate secondary structure elements in an individual subunit of an icosahedral virus from a cryo-reconstruction. I have the entire virion in pif format and would like to use the density from a single subunit using SSEHUnter and SSEBuilder. I am not sure how best to get the volume data as a useable mrc input for this tool. I tried using the volume eraser to eliminate other areas in the map that are not the subunit I'd like. When I save the map and then the session, the subunit looks fine in the session, but if I open the subunit mrc file in a new session, I get what appears to be inverse density (the stuff I erased), and in the volume viewer, the density looks inverted. If I move the slide bar to the left, I end up with a solid cube. I am either doing something horribly wrong, or this is maybe not the best method for excising my subunit??? Please advise the best approach to creating a subunit mrc file that can be used by SSEHunter. Thanks in advance! Kristin Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038