VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 30 2022 - 14:45:43 CDT

Carlos,
  Tachyon doesn't (yet) do the solid clipping plane behavior because
the existing versions don't yet implement CSG (constructive solid geometry)
operations (e.g. union, intersection, difference). In the short term,
POV-Ray is still the way to go.

I'd been holding off until now as I was doing a complete rewrite
of the GPU version recently.
CSG operations (even just the tiny subset needed for a solid clipping plane)
impose some extra per-ray bookkeeping, which for a CPU is no problem, but
for a massively parallel GPU comes at a higher cost.

Since VMD performs clipping on a fairly coarse per-representation basis,
it should be possible to support this on GPUs without incurring
unacceptable overhead costs. Since the Tachyon GPU code already makes
significant use of C++ template specialization, I don't think it would hurt
to add the required CSG functionality as another dimension of specialization
that triggers execution of a "CSG-capable" code path at run time.

I'll add this to my TODO list for Tachyon and see how it goes in the
GPU code first.

Best,
  John

On Tue, Aug 30, 2022 at 01:42:58PM -0400, Carlos Simmerling wrote:
> John - is there any way to get this behavior (solid clipping) in tachyon
> as well? thanks
> On Tue, Aug 30, 2022 at 1:33 PM John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â At least with the original versions of POV-Ray that we developed the
> VMD code against, the color obtained from the solid style clipping plane
> was determined by the objects that are cut/sliced by the plane.Â
>
> As an example, if you have a bright red atom cut open by the clipping
> plane,
> instead of being shown as a hollow sphere with interior shadowing,
> it should instead show the atom with a flat cut surface, with the
> same "bright red" color/material on the uncut parts of the same atom.
>
> If you're getting a result that's significantly different from what I've
> described there, then it may be a new/different behavior of later
> versions of POV-Ray, or some kind of unusual issue with your specific
> scene.
>
> When using ray tracing engines and other outboard renderers, it is
> important to ensure that you don't have the same atom(s) drawn twice
> with different colors/materials. In the VMD OpenGL display this may
> result in a scene that seems "okay", because the drawing order will
> determine which one is visible. But when rendered with a ray tracer,
> you may see dark/black surfaces, "cracks" on the atoms, or other
> artifacts
> associated with having identical geometry drawn on top of itself in the
> same
> place in space. Make sure you don't have any such duplication...
>
> Best,
> Â John
>
> On Tue, Aug 30, 2022 at 11:10:42AM -0500, Prateek Bansal wrote:
> > Hello VMD Users,
> >
> > I was trying to use clipping planes to show a cross section of my
> protein.
> > I used "Render as soid color" option in POV-Ray to set a solid color
> for
> > the clipping plane, as it helps me clarify the representation. I
> have been
> > trying to customize the solid color by going through the options in
> > pov-ray, but have been unable to do so. Does anyone have any
> > tips/workarounds for choosing the solid color that POV-Ray renders the
> > clipping plane as? The default I get is a smoky gray color for the
> solid
> > color.
> >
> > I am using MacOS 10.15 (Catalina) and VMD 1.9.4a51.
> >
> > I apologize if a similar question has been asked before, I couldn't
> find a
> > thread discussing this issue in particular.
> >
> > Thank you!
> >
> > Prateek
>
> --
> Research Affiliate, NIH Center for Macromolecular Modeling and
> Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [2]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â
> [3]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. http://www.ks.uiuc.edu/~johns/
> 3. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
Research Affiliate, 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/           
http://www.ks.uiuc.edu/Research/vmd/