Hi Jason,

> With shaders enabled, it seems that transparent sticks aren't rendered 
> correctly. The transparency setting seems to be under applied, and way way 
> under applied for stick surfaces directly facing the lighting. Setting 
> sphere_transparency to 0.5 produces nicely transparent spheres, but with 
> stick_transparency set to 0.5 the sticks are still opaque. I have to got to 
> 0.8 to see any significant transparency. And with stick_transparency = 1.0, 
> where I would expect to not see anything, it looks like the surfaces that 
> directly face the lighting are still drawn opaque. This results in really 
> strange looking displays. With use_shaders = 0 the sticks and spheres behave 
> the same and everything looks as I would expect.
>
> I see this behavior in both the incentive builds and the open source version.
>
> Are there settings that control the shader behavior, or do I have to mess 
> with the code in data/shaders?

The new basic shaders don't yet support transparencies.  They're there
basically to complement the volumes and will be further developed
soon.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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