[Chimera-users] SSEHUnter and SSEBuilder questions

[Kristin Parent]

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