I’m trying to visualize a section of the inner workings of the ribosome. To this end I’ve generated a surface and clipped it to reveal the internal structure I want to look at. This looks really good in the normal openGL view. When I raytrace it however, the part that’s clipped away still throws a shadow, so everything is completely dark. I know I could turn shadows off, but I’d really like to keep them for things that’s visible.
I also tried exporting to PovRay, but unfortunately the clipping plane isn’t really implemented in the export methods I tried (using the renderer=1 command and the script from http://adelie.biochem.queensu.ca/~rlc/work/pymol/ ).
I can extract the coordinates for the plane and put it into pov-ray, but because the surface is exported as thousands of little mesh2 objects, I can’t seem to explain to povray that they should all be “clipped_by” the plane. If I make a union or merge of the mesh2 objects, it works, but this is not a realistic solution, as the processor time needed is massive, even for simple test objects.
Does anyone have suggestions to fix this, using either the internal renderer og pov-ray?