3-D printing of chemical structures

Discussion in 'General Discussion' started by eperlste, Sep 26, 2012.

  1. eperlste
    eperlste New Member
  2. mkroeker
    mkroeker Well-Known Member
    A "pay-per-use" stock picture of the desired structure is only semi-relevant to your question.
    Head over to Bristol university's molecule of the month collection at
    , find the Methamphetamine entry in the table and select its "vrml" version
    (the "V" behind the name).
    Among the text, you will find a few illustrations of the molecule - click on them to download the 3d version.
    This file format should be printable on shapeways, even in color.
  3. eperlste
    eperlste New Member
  4. mkroeker
    mkroeker Well-Known Member
    Did you check the link in my message ? While the chemical formula on that page is a conventional line drawing, the VRML (extension .wrl)
    file it links to is the color-coded 3D ball-and-stick model you want, and should be directly uploadable to shapeways.
  5. eperlste
    eperlste New Member
    I did! But it still wasn't clear to me that displayed image would be different than the .wrl file. Sorry, I'm a little slow, I guess!

    Thanks for clarifying!
  6. eperlste
    eperlste New Member
    So I downloaded the .wrl version of the meth molecules from the link you suggested. The resulting files were 52kb in size. When I tried to upload them to Shapeways, I got an error.

    Assume that in these matters you're dealing with a small child. Can I draw a structure in ChemDraw, export it, open it in Meshlab, and create a 3D compatible file?
    JACANT Well-Known Member
  8. mkroeker
    mkroeker Well-Known Member
    I see that JACANT beat me to it, thanks. :)
    Regarding ChemDraw - probably yes, if it can export true 3D coordinates in the PDB format originally created
    for the Protein Data Bank ("true" 3D coordinates in the sense that they contain more than just the flat drawing
    with z=0 - I do not know ChemDraw's capabilities). The import options of meshlab for pdb appear to be quite limited,
    apparently it will create a "space-filling" model, but not a ball-and-stick one. The freeware RasMol program, however,
    should allow you to generate the kind of VRML file you want from a PDB one.
    Another alternative might be to try to find data from a crystal structure determination, e.g. in the "Crystallography Open
    Database" and work from there.
  9. 7777773
    7777773 New Member
  10. eperlste
    eperlste New Member
    Hello again. It's the idiot who's never used MeshLab or done any 3D printing. The good Samaritans on this forum directed me to the correct file: http://www.shapeways.com/model/723440/methamphetamine.html

    Now I would like to make the object 50% smaller. What's the easiest way to do that in MeshLab? Thank you!
  11. mkroeker
    mkroeker Well-Known Member
    Filters -> Normals, Curvatures and Orientation -> Transform:Scale
    Set "XAxis" to 0.5, make sure that "Uniform Scaling" is checked, check
    the "Preview" box if you like, then click on "Apply" if you are satisfied with
    the settings.
  12. mkroeker
    mkroeker Well-Known Member
    Oh well... VRML export from meshlab appears to be broken. And that wrl file is overly
    complex anyway - one extremely detailed mesh that just represents a tiny blue sphere
    that once must have been the anchor point for switching between the several viewer
    positions in the file. (And the molecule itself is a single mesh, not a collection of vrml
    "sphere" and "cylinder" primitives that would facilitate changing individual radii...)
    Try this one here instead http://shpws.me/k9gC - i have removed
    the unnecessary viewpoints and the selector sphere, and added a scaling transformation
    at the top. Just open it in a text editor, find the line that reads "scale 0.5 0.5 0.5" and change
    it if necessary. (With this scale, an upload specifying "Inch" as the base unit results in a
    model that is 5 by 2.1 by 1.8 in and would cost something like $15 in "full-color sandstone"
    or $20 in paint-it-yourself WSF plastic.
  13. JACANT
    JACANT Well-Known Member
    Please see updated file, half size. http://www.shapeways.com/model/728611/
    As mkroeker pointed out there is a small isolated sphere approx .7mm. You can just see it in the center of the image. I don't think this will affect the print. Surely it will just get lost in the printing process. You could ask service@shapeways.com