Hello Lawrence, You may want to use Per-Model Clipping (in menu under Tools… Depiction, or as command "mclip"): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html> Just make sure to specify the model that is your cryoEM surface. Whereas the global clipping planes in the SIde View affect everything and are always perpendicular to the line of sight, you can interactively position a per-model clipping plane at any angle, and it only affects one model (although each model can have its own). You can also erase an octant with "vop ~octant" and erase all but that octant with "vop octant" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 16, 2013, at 11:35 AM, "Tartaglia,Lawrence J" <ltartaglia@ufl.edu> wrote:

Hello,

I have a cryoEM map of a virus that I'm visualizing in chimera. I'd like to get a perfect cross-section of the map that I can use for publication. I've used the "side view" tool, but I can't get an exact cross-section. Are there any options to achieve this?

Thanks!

Best,

Lawrence -- Lawrence J. Tartaglia, Ph.D. Postdoctoral Scientist Agbandje-McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine, University of Florida