(Where you wrote mesh, you meant surface right?)

        PyMOL's OpenGL renderer does a poor job of combining transparent
objects, but the ray-tracer should be capable of doing this so long as
multi-layer transparency is enabled.  This may or may not be acceptable
given all additional geometric elements you will end up with as a result.

See example image at:

To achieve this, adjust the settings as follows:

set transparency, 0.5
set cartoon_transparency, 0.9
set transparency_mode, 1
set backface_cull, 0
set two_sided_lighting, 1
set ray_shadows, 0


Of course, an alternative is to really use a see-through mesh, instead of a

Default settings +

set ray_shadows, 0
set min_mesh_spacing, 0.4
set cartoon_transparency, 0.55


> -----Original Message-----
> From: 
> [] On Behalf Of Paul Wan
> Sent: Friday, February 20, 2004 7:37 AM
> To:
> Subject: [PyMOL] Cartoon Transparency AND Transparent Mesh
> Hi
> Just got my hands on Pymol G5 version and having loadsa fun with it.
> I'm trying to make a diagram and wondered if it is possible 
> to make the cartoon transparent then put a mesh over the 
> whole thing (also made transparent).
> Currently I can make th ecartoon transparent but as soon as I 
> add a mesh (no matter what the transparency level) I loose 
> the Cartoon ribbon.
> Is there anyone out there that can help me do both?
> Thanks
> Paul

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