Large scale 3D printing

A more hands-on way of visualizing macromolecular molecules, is by 3D-printing. Companies like have long offered easy and relative affordable access to 3D prining of molecular molecules based on PDB files. However the affordable part only holds true for relative small 3D models and there is also an upper limit to the max dimensions they can print your model in.

So to get a model in a “display worthy” size, I had to find some people with a big 3D-printer which were up for a challenge. The local engineering department had just the guys for this. A couple of students had build their very own 3D-printer capable of printing volumes larger than a cubic meter.

The DIY 3D-printer they built:
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Small-scale print of an early version of the print, where an accompanying membrane for the model to stand on top of was included. However the membrane did not make into the final model.

2D footprint of the final build size (engineer hand for scale):
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1/4’ish  of the way, notice the amount of support material needed to enable printing of the “arms”:

Time-lapse movie of the actual print process. NB. it is not the most action packed video, hence I added some music just to make it durable to get through:

Final model after the support material had been removed (standard lab equipment for useless scale):

Got a post.doc in a neighbor lab to paint it with an airbrush which worked out quite well (though not the best photo):

I am very happy with the final result, not only is the model itself very complex and impressive, but the actual size of the model is what really makes it stand out from other 3D-prints I have seen of molecular molecules.

7 thoughts on “Large scale 3D printing”

  1. Hey Ruki, this 3D printing process is impressive. One question, how did you transform the PDB file into a format compatible with the 3D printer?

    1. Hi David,
      Yeah I am also quite happy about the print myself. I was actually planning to write a detailed post about how I prepared the model for printing etc. And I will still do that, but I can give you the cliffnotes here. There are many ways of doing this, so I will just tell what I did but eventually it depends on what formats the 3D-printer reads.

      I assume you know your PyMol or Chimera (otherwise just ask)? Anyway I used Pymol, though Chimera should actually be better as it can export PDB files to the format you want .stl, unfortunately I just hate that program, so I dont use it.

      Anyway I opened my PDB file in PyMol, selected the molecules I wanted to print, displayed them as a surface rendering (best for 3D printing) and exported/saved them as a .wrl file (the vrml wireframe format). I then use a free program called Meshlab ( to both convert the .wrl format to .stl but also to do Polygon reduction ( to lower the size of the final file. Which was really needed for this specific model, as it initially was around 1gb total and the engineers prefeered below 100mb.

      here is a tutorial for meshlab if you dont know that program (it is very easy to use):

      There are also some great guides on creating 3D models for printing here:

      or at least there used to be, I didnt check just took the link from a bookmark.

      Hope this helps, otherwise just ask


      1. Thanks for getting back to me so quickly. I was only aware of using Chimera to export to STL. Pymol -> Meshlab -> STL sounds like a better option.


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