[Chimera-users] Volume transparancy

Dougherty, Matthew T matthewd at bcm.edu
Wed Aug 2 11:05:11 PDT 2017

another approach is to disable the display of the model at frame 101.

This will remove the defects and improve your overall graphics computation.

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, August 2, 2017 12:56:07 PM
To: Matzov Donna
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Volume transparancy

Hello Donna,
Unfortunately multiple transparencies often don’t work well together.

I would use “movie crossfade” instead of ribbon transparency.  In that case, you wouldn’t be able to have the scene moving (rotating, zooming, etc.) at the same time,  since the crossfade is simply a pixel-for-pixel interpolation.  When the scene is not moving, specify a crossfade transition between ribbon hidden and ribbon shown.  You can specify the number of frames.

<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_movie.html-23crossfade&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=ibveGQtX1lCuoaFiArA0sEc8t3VwtUdnLsy94Nbyhyo&s=-jr8KfzTGkEzQcqRDDt4aswmQsD-4e8MGLRoeCxCSi8&e= >

It will show up in the recorded movie even though not shown on the screen.

In our next-gen software ChimeraX, however, there is a “crossfade” that is shown on the screen: <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_docs_user_commands_crossfade.html&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=ibveGQtX1lCuoaFiArA0sEc8t3VwtUdnLsy94Nbyhyo&s=8Nt7RdQ5S_n4HOfTLIiqiO0L-jqPCWVE_al89ekfBrU&e= >

Another possibility for avoiding multiple transparent models is showing the surface as mesh, but then you would probably need to tinker with mesh fineness, linewidth, and lighting.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 2, 2017, at 4:37 AM, Matzov Donna <matzov.donna at weizmann.ac.il> wrote:
> Hello,
> I'm trying to make a movie such that a ribbon model would appear while its maps (represented as surface) is already shown and is partially transparent. For that I wanted to set the ribbon transparency to 100 and then use the following command:
> transparency 0,r frames 100
> The problem is that when when the ribbon in 100% transparent, the shape is still apparent in the partially transparent map. the ribbon shapes are not seen only when the map is not transparent at all.
> Is there a way to fix that?
> Thanks,
> Donna

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