[chimerax-users] Transparency bugs with ribbons and density maps

[Elaine Meng]

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 at 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