POV-Ray also works extremely well as a distributed job. This site has some basic discussion of some of the distributed POV options: http://columbiegg.com/httpov/?p=why Jonathan

Today's Topics:

1. (no subject) (jean-francois menetret) 2. Re: Flip handedness of map (Tom Goddard) 3. VRML alpha vs 1-alpha (Nils Becker) 4. Re: VRML alpha vs 1-alpha (Greg Couch)

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Message: 4 Date: Tue, 22 Jan 2008 10:37:54 -0800 (PST) From: Greg Couch <gregc@cgl.ucsf.edu> Subject: Re: [Chimera-users] VRML alpha vs 1-alpha To: Nils Becker <nils.becker@ens-lyon.fr> Cc: chimera-users@cgl.ucsf.edu Message-ID: <Pine.OSF.4.63.0801220934340.1761700@guanine.cgl.ucsf.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

On Tue, 22 Jan 2008, Nils Becker wrote:

...

Hi,

I found information on the web site that VRML models use 1-alpha blending for transparency, and that that looks ugly. I agree.

Now I have externally generated VRML files including transparency.

Is there a way to get nice (normal) transparency rendering of these models in chimera?

e.g. editing the vrml files, converting them to another format or some option inside chimera?

Thanks for any help, cheers, Nils

The VRML transparency is 1-alpha, because alpha is an opacity value. So that is just an alternative way of saying that same thing, and is not the reason it is worse.

The reason VRML transparency is worse is that there is no sorting within the VRML shapes, so the blending of transparent objects has to be drawing-order independent, so VRML uses additive blending.

The simpliest solution would be to live with chimera's current depiction and use the Save Image dialog to generate a ray-traced version. The ray-traced version will be much nicer (and take a lot longer to compute, try using the POV-Ray 3.7 beta on a multi-core computer to speed things up).

The other solution, is to write some Python code and use the _surface module's Surface_Model and Surface_Group classes. That is, convert each VRML object into a triangulated surface, a Surface_Group, and put all of the Surface_Groups into one Surface_Model. All surfaces within one Surface_Model are sorted so that the transparency is correct for more than one overlapping surface (unlike the transpareny in chimera between models that only works for one level of transparency). You can see examples that use the _surface module in the GraspSurface, IMOD, Icosahedron, and Intersurf modules (and others) in the CHIMERA/share directory of your installation.

If you have any questions about the _surface module, please ask them on the chimera developers mailing list, chimera-dev@cgl.ucsf.edu.

Greg Couch UCSF Computer Graphics Lab

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