Hi Jacob In Pymol, have you tried adding in a direct light source? e.g.
set direct, 0.5 It worked nicely in a similar situation for me Daniel On Wed, 2005-11-23 at 11:42 +0100, Jacob Poehlsgaard wrote: > Hi folks > > > > 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? > > > > Sincerely > Jacob Poehlsgaard > > SDU, Denmark > > -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
