From: Axel Kohlmeyer (
Date: Sun Dec 11 2011 - 18:09:43 CST

On Sun, Dec 11, 2011 at 6:56 PM, Töre Han Balta <> wrote:
> Hi,
> I'm using vmd-1.9 on a 64bit Fedora distribution of linux.
> Here is "uname -a "Linux localhost.localdomain #1 SMP
> Fri Nov 11 21:36:28 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
> I've attached is the vmd script and pdb file that I'm trying to take
> snapshot of the screen.
> I have also attached images ans images named as to have correspondence with
> the render method. I converted images to jpg to reduce size.
> In the *.vmd file, there are three representation of the molecule with
> different coloring options.
> I am trying to render the screen image, but tachyon methods just renders
> image as if there is no representation except the first one.

thanks. this is a pretty complete description.

> Could it be a GPU driver problem?

no, this is a user error.

you have multiple representations of the
same type for the same atoms with *exactly*
the same size options. with OpenGL the latter
representations show up "on top" due to the
way OpenGL is implemented, but effectively
you are depending on undefined behavior.
raytracing software handles these cases
differently, so you get a different output.

to get what you want, you just have to remove
the ambiguity, e.g. by setting the "Sphere Scale"
and "Bond Scale" parameters in the first representation
to something smaller than what you using in the
second and third, or enlarge the radii in the latter two.

this is neither a bug in VMD nor in any driver.
the data is all there and being processed.


Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.