Certain newer Raster3D objects are ignored, such as quadrics. Also, nearly all of the header information is ignored--most notably, the viewing matrix.
Aside from quadrics, VMD can read and display all shapes in the format with one exception. Raster3D uses many cylinders with spherical (rounded) ends. VMD deliberately omits these rounded ends since the resultant image would be very slow.
Finally, since VMD uses a palette of 16 colors, each triplet is converted into its ``nearest'' indexed color. This may cause images to be colored slightly differently than expected.