From: Anthony Ruth (
Date: Thu Apr 02 2020 - 14:46:33 CDT


Is there a way to make VMD display dangling bonds?
For example, I would like to take a structure like this one and break it
down by color:

[image: image.png]
So there would be 3 separate pieces, one for each color. Each piece would
contain the spheres and the half of the bond which is nearest that atom.
e.g. just this for the top hydrogen:

[image: image.png]

I cannot find a way to make only half the bond show (The half nearest
the hydrogen).
What I am really planning to do is use a 3d printer to print different
colors for different atoms. To do that I would need separate .STL files for
each color. Then I can load them into the printing program one at a time
and assign each a different material. Conceptually it is very similar to
the way the image is shown above where the different parts of the image are
assigned different colors.

Does anyone have an idea how to do this? I thought maybe the model could be
exported to contain the 3D information and then another program could split
it up by color.

Anthony Ruth
Condensed Matter Theory

image.png image.png