I've been doing a lot of analysis rendering over proteins in Chimera lately.  Bild (via VRML) has worked quite well for this.  I wanted the ability to specify a transparency value (from 0 to 1) for the shape objects (boxes, arrows, etc.).  The attached patch 'bld2vrml.diff' adds a .transparency 'command' to the bild format that sets the 'transparency' attribute on subsequent objects' 'Material' element in the generated VRML.  A sample input file 'test.bild' (see below) and image 'test.png' are also attached.

Example input below:
.color green
.transparency 0.0
.box 5 5 5 10 10 10
.transparency 0.25
.box 0 0 0 5 5 5
.transparency 0.5
.box -5 -5 -5 0 0 0
.transparency 0.75
.box -5 -5 -5 -10 -10 -10
.transparency 0.9
.box -10 -10 -10 -15 -15 -15

--
David A. C. Beck, Ph.D.
dacb@u.washington.edu
Valerie Daggett Laboratory
University of Washington, Seattle<bld2vrml.diff><test.bild><test.png>_______________________________________________
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