Hi Jacob, Many thanks for your answer. Here is the follow-up: I tried to exclude the "load" commands from my script, to pre-load the structures, display them, be sure that no other windows were overlapping the PyMol display window (I even placed the PyMol window on another location on my screen!), and it didn't change anything. I also tried to add the "ray" function before the "png" function and there the image is complete... I don't understand the reason... But as I generate quite a lot of pictures and still working on my script I dont want to spend hours waiting all the frames being ray-traced!!
Grégori
