From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 15 2014 - 09:17:07 CDT

Hi,
  If you want the interior brighter, your easiest options include increasing
the AO ambient and AO direct scaling factors, or choosing colors that are
brighter to begin with (e.g. "pastel" or "washed out" colors that have a
high white content and a relatively low to moderate amount of color saturation).

The glowlights script is sort of an expert-level means of placing
positional lights in a specific part of a molecular structure so that
you can add more targeted lighting. The glow lights are omnidirectional,
but to make them useful for this purpose, they have distance-based
attenuation equation that has constant, linear, and quadratic terms
that you specify when the light is defined. By defining a light that has
significant quadratic attenuation, you can make its effect highly
localized, which is not something that you could do with either the
normal VMD directional lights, nor the AO lighting. The current limitation
with these glow lights is that to be useful to an end user, they have to
be specified in model coordinates (e.g. cartesian coords of the molecular
structure), but VMD and Tachyon have to use the lights in world coordinates,
so there's some complex machinery involved in sorting out their coordinates,
and at the moment this machinery is not part of the core of VMD, so to use
them effectively requires more VMD scripting than I would like.

My plan is that I will soon be moving the logic for the glowlights into
the core of VMD itself, and that it will be implemented both in the
interactive OpenGL code path as well as the ray tracing engines such as
Tachyon, so the effects of the glowlights can be interactively viewed,
tweaked, and so on, and they could be used just as easily in a live demo
as in a batch movie rendering. The catch is that while there's no limit
on the number of such lights one could use in something like Tachyon, there
are significant limitations on how well this works in OpenGL, and I will
have to work through a minefield of driver bugs as I push VMD's OpenGL
GLSL shaders further into areas where some vendor's drivers have had
problems in the past. That said, I'm hoping that the drivers have all
gotten significantly better, and that many of these past driver bugs
are now "water under the bridge" as they say.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 15, 2014 at 09:39:39PM +0800, Kevin C Chan wrote:
> Thanks Stone, it looks much better now. Do you also have suggestions for the materials of the protein inside the transparent surfaces? Now I am using Diffuse and AOs as suggested on the webpage.
>
> Also I could not quite get how the two light coefficient works, what is the difference among them and your glowlight.tcl (appeared in the mailing list) if what I want is light up the protein inside the surfaces only.
>
>
> Cheers,
>
> Kevin
> ukevi_at_gmx.hk
> On 13 Oct, 2014, at 21:59, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > I would suggest that you try using the "GlassBubble" material for
> > your transparent surface. It should case only very weak shadows, but
> > it will hopefully clearly show the interesting boundaries of the
> > outer molecular surfaces without obscuring interior cartoon representations.
> > Give that a try and tell us what you think...
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Mon, Oct 13, 2014 at 09:48:21PM +0800, Kevin C Chan wrote:
> >> It gives shadows from the curved surface which confuses with the cartoon
> >> representations underneath.
> >> Kevin
> >> [1]ukevi_at_gmx.hk
> >> On 13 Oct, 2014, at 14:52, Norman Geist
> >> <[2]norman.geist_at_uni-greifswald.de> wrote:
> >>
> >> What exactly does *less satisfactory* look like?
> >>
> >> Norman Geist.
> >>
> >> Von: [3]owner-vmd-l_at_ks.uiuc.edu [[4]mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> >> Auftrag von Kevin C Chan
> >> Gesendet: Montag, 13. Oktober 2014 06:39
> >> An: VMD Mailing List
> >> Betreff: vmd-l: Transparency rendering by Tachyon
> >>
> >> Dear VMD users and Stone,
> >>
> >> I am currently encounter questions about Tachyon image rendering in VMD.
> >> Refer
> >> to [5]http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/, I am
> >> very pleased by turning on AO. However whenever a transparent surface is
> >> present, it is less satisfactory. I have browsed the mailing-list and
> >> tried options like trans_vmd but it does not help much.
> >>
> >> Can anyone share some experience on rendering images involving
> >> transparency, for instance, a transparent surface of the protein outside
> >> its cartoon representation?
> >>
> >> Thanks so much.
> >>
> >> Kevin
> >> [6]ukevi_at_gmx.hk
> >>
> >> ---------------------------------------------------------------------------
> >>
> >> [7][IMG] Diese E-Mail ist frei von Viren und Malware, denn der [8]avast!
> >> Antivirus Schutz ist aktiv.
> >>
> >> References
> >>
> >> Visible links
> >> 1. mailto:ukevi_at_gmx.hk
> >> 2. mailto:norman.geist_at_uni-greifswald.de
> >> 3. mailto:owner-vmd-l_at_ks.uiuc.edu
> >> 4. mailto:owner-vmd-l_at_ks.uiuc.edu
> >> 5. http://www.ks.uiuc.edu/Research/vmd/minitutorials/tachyonao/
> >> 6. mailto:ukevi_at_gmx.hk
> >> 7. http://www.avast.com/
> >> 8. http://www.avast.com/
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
>
>

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/