Hi Pascal, Unfortunately, it is a known limitation in both Chimera and ChimeraX that multiple transparent models together are often rendered incorrectly.
Tom Goddard explains it in a little more detail in this previous post: http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html
Your image looks especially weird because one of the layers (ribbon) is completely transparent.
I sometimes try to avoid having multiple transparent models by making a surface model mesh instead instead of transparent, but that may not give the appearance you would like, sorry. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 27, 2019, at 8:22 AM, Pascal Albanese pascal.albanese@polito.it wrote:
Dear all,
I'm haviong troubles with visualization of trasnparencies when using EM maps and PDBs. See in the example here: <image.png> The ribbon in the front is completely transparent (with silhouettes), the surface is set with a 50% transparency, and the pseudobonds inside or behind can be only visible when transparency of pbonds is set to 0 (at 5 already they disappear). Does anyone already experience these issues?
Bests, Pascal