From: John Stone (
Date: Wed Aug 06 2014 - 09:50:09 CDT

Tristan's note about some reps not looking very nice as a "glow"
when rendered with transparent materials is a pretty good point.
If we really wanted to make a "glow" representation, it would likely
be best to implement something along the lines of a QuickSurf
representation, but rather than having a triangulated surface boundary,
we could render the density field itself, rather like an X-ray where areas
of high density are opaque and areas of low density are translucent or
transparent. By doing something like this you would get a "fuzzy" "glowing"
boundary associated with the linear combination of Gaussians, and the user
could have similarly easy-to-use controls over radius and density
scaling factors to make this "halo" look the way they want.
I have been planning on implenting a number of new volumetric rendering
capabilities in VMD. If I implemented a volume ray caster for the
density map produced by QuickSurf, that would probably get 90% of
what is needed to do this well and it would have the benefit of
being useful for other volume visualizations as well. I'll keep this
in mind for the next version after this one.

  John Stone

On Wed, Aug 06, 2014 at 10:21:04AM -0400, Josh Vermaas wrote:
> What I do is similar to what you have tried. The trick I've found is to
> make the transparent representation only infinitesimally larger (3.001 vs
> 3 for the radius for instance), which you'll need to setup with the
> tkconsole, as the gui doesn't give you the resolution you need to make it
> look good. From there you usually need to play with the materials to give
> the right effect (I personally think that transparent uses too much
> ambient lighting, but thats personal preference). Keep in mind that you
> can play with your shaders (Display->Rendermode->GLSL) so that transparent
> doesn't look hideous in the OpenGL window too to make manipulating the
> materials easier to judge.
> -Josh Vermaas
> On 8/6/14, 2:49 AM, Tristan Croll wrote:
> I'm trying to find the best way to visualise residues by some property
> (e.g. conservation, favourability score on the Ramachandran plot, charge
> ...) while still keeping standard CPK colouring to make the residue
> types easy to recognise. Just wondering, how hard would it be to add a
> visualisation that makes the atoms "glow" with a colour set by the beta
> or occupancy column? The effect I'm thinking of is rather like the image
> on the front page of I can get a reasonable effect by using a
> licorice representation in CPK, and overlaying that with a thicker but
> transparent representation with my desired colouring, but transparent
> licorice doesn't render at all well.
> Cheers,
> Tristan

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