> i've just created many CGOs, which show up solid surfaces like spheres and > ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 > and leave the others solid? > I've checked out the reference and the manual, and found something like:
The CGO support in Pymol does not quite seem to be all there; I had CGOs appear correctly in raytracing some of the time, other times they just would not render at all. I needed transparency, too, so I ended up exporting everything to Povray and rendering the image there. This requires some familiarity with Povray, because the material definition for the transparent surfaces needs to be written manually and the CGOs must be found in the Povray input that Pymol spews out (80 MB of text in my case...). One way to do this is to write out the CGOs in one Povray file and the molecules in another. With Povray you can get shadows on CGOs and molecules inside transparent CGOs to render correctly, which is not really possible in 2D (Photoshopping or such). Mikko
