From: John Stone (
Date: Fri Apr 03 2020 - 10:58:36 CDT

  STL files do not have any material information. The original STL spec
contains only triangle surface information. STL is the oldest file format
used for 3-D printing and is very low-tech. If you want colors and/or
other shading/material information, I would suggest exporting the scene
using X3D, or Wavefront OBJ. I would think any modern printing software
would be able to import these or other more modern file formats.


On Fri, Apr 03, 2020 at 10:29:06AM -0500, Anthony Ruth wrote:
> 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 <[1]>
> wrote:
> 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.¬ [2]¬ 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
> <[3]> 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:
> [4]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:
> [5]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
> References
> Visible links
> 1.
> 2.
> 3.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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