Paul, (Where you wrote mesh, you meant surface right?)
PyMOL's OpenGL renderer does a poor job of combining transparent objects, but the ray-tracer should be capable of doing this so long as multi-layer transparency is enabled. This may or may not be acceptable given all additional geometric elements you will end up with as a result. See example image at: http://www.pymol.org/ex/040220A.png To achieve this, adjust the settings as follows: set transparency, 0.5 set cartoon_transparency, 0.9 set transparency_mode, 1 set backface_cull, 0 set two_sided_lighting, 1 set ray_shadows, 0 ray Of course, an alternative is to really use a see-through mesh, instead of a surface... http://www.pymol.org/ex/040220B.png Default settings + set ray_shadows, 0 set min_mesh_spacing, 0.4 set cartoon_transparency, 0.55 Cheers, Warren http://delsci.com/macpymol > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Paul Wan > Sent: Friday, February 20, 2004 7:37 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Cartoon Transparency AND Transparent Mesh > > Hi > Just got my hands on Pymol G5 version and having loadsa fun with it. > I'm trying to make a diagram and wondered if it is possible > to make the cartoon transparent then put a mesh over the > whole thing (also made transparent). > > Currently I can make th ecartoon transparent but as soon as I > add a mesh (no matter what the transparency level) I loose > the Cartoon ribbon. > Is there anyone out there that can help me do both? > Thanks > Paul > >