[Chimera-users] Z-slice transparency

Tom Goddard goddard at cgl.ucsf.edu
Thu Nov 15 19:13:24 PST 2007

I met Lu in San Diego and found out he was showing a volume slice and a 
second model which was also a volume using solid rendering style.   The 
trouble is that Chimera cannot correctly display two transparent models 
-- at most one can be transparent.  If two are transparent, the last one 
drawn (higher model id number) always appears on top of the other 
transparent models.  This is a (serious) limitation of the Chimera 
graphics architecture.

Technically Lu has the single plane set to be completely opaque, but all 
solid rendered volumes are rendered as if they have transparency even if 
the coloring is set for complete opacity.  (The OpenGL z-buffer which 
records the depth of visible objects and prevents obscured surfaces from 
being shown is not used with "transparent" rendering).  We tried using 
the TomoPlane Chimera extension from Karin Gross and Christoph Best and 
that draws truly opaque volume planes, but it is much slower.


Lu wrote:
> Hi Tom,
> I tried everything that you mentioned, including adding multiple 
> points to the histogram, but I can still see stuff through the 
> Z-slice. Anyway, I noticed that you're going to be at the Scripps EM 
> workshop next week. If you have time at the workshop, I'd be happy to 
> show you the type of Amira movie that we'd ultimately like to make 
> using Chimera.
> Cheers,
> -Lu

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