From: John Stone (
Date: Tue Aug 30 2022 - 11:42:31 CDT

  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

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...


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