[Chimera-users] Dual transparency in chimerax

[Elaine Meng]

P.S. maybe in Chimera, you could try using “molmap” to make a surface for the rRNA, as in #3 in the surface workarounds page:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

That only solves part of the problem, however, as the multiple transparent layers may not be rendered correctly.

> On Nov 20, 2018, at 10:32 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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.
> Elaine
> 
> 
>> 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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