Hi Tom,
A first step would be to make Chimera volume display able to use mask files that are produced by segmentation done with programs.
A segment file would be another grid with integer values specifying the segment of the particular voxel. Density would be then divided into subsets that could be treated as separate grids. Of course, one can also do this outside chimera, and just read in multiple grids. More generally, a nice concept would be the possibility of mapping values from one grid to an isosurface calculated from another grid. The isosurface would be then colored based on the mapped values. The mapped value could represent a voxel belonging to some segment, or distance to some other voxel (e.g. center of the model) etc. Cheers, Juha