Dear pymol users, I got an answer from several helpful people: I had somehow disabled the depth cue in the raytracing rendering:
----- There are two settings that give you an impression of depth. depth_cue for the OpenGL display and ray_trace_fog for the ray tracer set ray_trace_fog, 1 to preserve the depth cue in your rendered image. ----- Ah, now it works beautifully! thank you! Anders -- Anders Østergaard Madsen Centre for Crystallographic Studies Department of Chemistry, University of Copenhagen
