Hi Yehuda, In Chimera, by default only a single transparentl layer is shown. You can turn it off with command “~set singleLayer” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> ...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects> However, even with this option turned off, multiple transparent surfaces are still often rendered incorrectly in Chimera, a known problem. You can try it and see how it looks in your situation. Unfortunately, this multiple-transparent-surfaces problem has not been solved in ChimeraX either, as detailed in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 8:55 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon