[Chimera-users] Dual transparency in chimerax

Yehuda Halfon yehuda.halfon at weizmann.ac.il
Tue Nov 20 10:05:13 PST 2018

Hi Elaine,

Thanks for the help, I have to use chimerax since the regular chimera can't do surface for rRNA.
Dose chimerax has a kinda workaround like that?

Yehuda Halfon

-------- Original Message --------
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, November 20, 2018 07:57 PM
To: Yehuda Halfon <yehuda.halfon at weizmann.ac.il>
Subject: Re: [Chimera-users] Dual transparency in chimerax
CC: chimera-users at cgl.ucsf.edu

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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