From: Anthony Ruth (
Date: Fri Apr 03 2020 - 10:29:06 CDT

I took a look at the .STL files and they do not save material information.
They are text files so they can be opened with a text editor. Maybe there
is another format which does save material information? VMD is so close,
but without a way to use half a bond (or have the color saved to an output
file), I do not see any way to attach the molecules together.

It appears the author of the multicolored protein models link used paints.

Anthony Ruth
Condensed Matter Theory

On Thu, Apr 2, 2020 at 3:55 PM Josh Vermaas <>

> Hi Anthony,
> Its been a while, but doesn't the .stl file VMD spits out have some
> material information in it already? I do recall that the stl files VMD
> makes are hollow, since it only tells you about surface elements, but that
> hasn't stopped others from making various multicolored protein models
> before, so in principle I think this should be feasible.
> Without
> drawing the graphics objects yourself, I'm not aware of a way to show only
> half a bond.
> -Josh
> On Thu, Apr 2, 2020 at 2:23 PM Anthony Ruth <>
> wrote:
>> Hello,
>> 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.
>> regards,
>> Anthony Ruth
>> Condensed Matter Theory

image.png image.png