Hi Jett, We are currently working on better (multi-level) transparency for all representations, this will be a feature for the next PyMOL release.
In the current PyMOL version, you may see two artefacts for semi-transparent spheres in real-time rendering: 1) The "shading" that you describe comes from unsorted triangles. This affects the old non-shader rendering, where spheres are made from triangles. I assume you use an older PyMOL version or a graphics driver which does not support shaders. 2) New shader based sphere rendering (PyMOL 1.6+) looks much better, but for two intersecting semitransparent spheres, only one of them will be transparent with respect to the other one. Ray tracing should show the correct transparency, so I wonder why it looks solid for you. PyMOL by default does single-layer transparency per representation (transparency_mode 2) Maybe you expect multi-layer, which would be transparency_mode 1: PyMOL> set transparency_mode, 1 Hope that helps. Cheers, Thomas On 12 Feb 2015, at 12:45, SongJianHui <gigi...@hotmail.com> wrote: > Hello, everyone, > > I've been trying use pymol to generate an image based on C-alpha coordinates > only. I tried to set the sphere to be transparency by the command "set > sphere_transparency, 0.5". However, the surface of the sphere shows some > shading which looks quite odd. If I ray trace the image, the surface looks > nice but it is solid rather than transparent. Any suggestions? Thanks. > > Best, > Jett Song -- Thomas Holder PyMOL Principal Developer Schr?0?2dinger, Inc. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
