[Chimera-users] Exporting surfaces as vrml

Greg Couch gregc at cgl.ucsf.edu
Fri Aug 28 11:46:12 PDT 2009

As you found out, VRML has limited support for transparency, and that is 
one reason why chimera's native export format is X3D.  VRML's transparency 
is limited to a single value per shape, and X3D's transparency can vary 
within a shape.  Tom's example only worked because the surface was of a 
single color.

FYI, if you are just interested in molecular surfaces, it should be fairly 
easy to extract the information you need out of the X3D file and write it 
out in whatever format your modeling program needs.

 	- Greg

On Fri, 28 Aug 2009, Tom Goddard wrote:

> Hi Christian,
> I'm not sure what version of Chimera you are using, but with the current 
> daily build, the VRML export (File / Export Scene...) does include 
> transparency of surfaces.  I believe older Chimera versions (1.3, ...) also 
> do this.  I made a transparent red icosahedron and writing as vrml
> shape icos div 1 color 1,0,0,0.3
> export format vrml ~/Desktop/test.vrml
> The resulting vrml text file does have the transparency information, and when 
> I open it in Chimera it is transparent (although Chimera does not display 
> transparency of VRML models correctly).  So quite possibly the program you 
> are using to read the VRML is ignoring the transparency.
>   Tom
> -------- Original Message --------
> Subject: [Chimera-users] Exporting surfaces as vrml
> From: Christian Hesketh
> To: chimera-users at cgl.ucsf.edu
> Date: 8/28/09 9:50 AM
>> Hi there,
>> I am trying to export molecular surfaces with varying transparencies to 
>> vrml, but the resultant model has a completely opaque surface. Is there 
>> anyway to export surfaces with transparent features to a 3D model? I would 
>> rather not work with x3d files as there don't seem to be any good 3D 
>> modeling programs that can accept this format.
>> Thanks in advance,
>> Christian
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