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<p dir="ltr">Hi Elaine,</p>
<p dir="ltr">Thanks for the help, I have to use chimerax since the regular chimera can't do surface for rRNA.<br>
Dose chimerax has a kinda workaround like that?</p>
<p dir="ltr">Yehuda Halfon </p>
<br>
<br>
-------- Original Message --------<br>
From: Elaine Meng <meng@cgl.ucsf.edu><br>
Sent: Tuesday, November 20, 2018 07:57 PM<br>
To: Yehuda Halfon <yehuda.halfon@weizmann.ac.il><br>
Subject: Re: [Chimera-users] Dual transparency in chimerax<br>
CC: chimera-users@cgl.ucsf.edu<br>
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<div class="PlainText">Hi Yehuda,<br>
In Chimera, by default only a single transparentl layer is shown. You can turn it off with command “~set singleLayer”
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html</a>><br>
...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section).<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects</a>><br>
<br>
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.<br>
<br>
Unfortunately, this multiple-transparent-surfaces problem has not been solved in ChimeraX either, as detailed in this previous post:<br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html">http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html</a>><br>
<br>
Best,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Nov 20, 2018, at 8:55 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:<br>
> <br>
> Hi all,<br>
> 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.<br>
> Is there a way to do it in chimerax?<br>
> Yehuda Halfon<br>
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