[Chimera-users] Dual transparency in chimerax

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 20 09:57:00 PST 2018

Hi Yehuda,
In Chimera, by default  only a single transparentl layer is shown.  You can turn it off with command “~set singleLayer” 
...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section).

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:

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 at 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

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