I met Lu in San Diego and found out he was showing a volume slice and a second model which was also a volume using solid rendering style. The trouble is that Chimera cannot correctly display two transparent models -- at most one can be transparent. If two are transparent, the last one drawn (higher model id number) always appears on top of the other transparent models. This is a (serious) limitation of the Chimera graphics architecture. Technically Lu has the single plane set to be completely opaque, but all solid rendered volumes are rendered as if they have transparency even if the coloring is set for complete opacity. (The OpenGL z-buffer which records the depth of visible objects and prevents obscured surfaces from being shown is not used with "transparent" rendering). We tried using the TomoPlane Chimera extension from Karin Gross and Christoph Best and that draws truly opaque volume planes, but it is much slower. Tom Lu wrote:

Hi Tom,

I tried everything that you mentioned, including adding multiple points to the histogram, but I can still see stuff through the Z-slice. Anyway, I noticed that you're going to be at the Scripps EM workshop next week. If you have time at the workshop, I'd be happy to show you the type of Amira movie that we'd ultimately like to make using Chimera.

Cheers, -Lu