From: Carlos Simmerling (
Date: Tue Aug 30 2022 - 12:42:58 CDT

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 <> wrote:

> Hi,
> 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.
> 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,
> 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