[Chimera-users] Dual transparency in chimerax

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 20 10:32:19 PST 2018

Oh, I didn’t realize you had to use ChimeraX for your system.  As far as I know, there isn’t a control for single-layer transparency in ChimeraX yet, sorry.

> On Nov 20, 2018, at 10:05 AM, Yehuda Halfon <yehuda.halfon at weizmann.ac.il> wrote:
> 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” 
> <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 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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