Preparing a Digital Molecule Model for 3D Printing




The last years we were able to improve our understanding of 3D structures of large molecules, e.g. nucleic acides and proteins, and how this relates to their function.

Nowadays, thank to resources like the Protein Data Bank or the Nucleic Acid Database, in combination with many molecule views and modifiers such as Pymol, Chimera, JSmol et cetera, three dimensional renders and animations of molecules can be created in no time.

Currently, it is not enough just to view the models, but actually 3D-print those molecules. In this article, we want to explain you how to prepare your digital model for 3D printing.

Reasons for printing 3D models of Proteins, Nucleic Acids, etc.

In most cases a 2D visualization can be sufficient, but there are also some cases where having an actual physical model can be more advantageous. This could be interesting for students for example who struggle imagining the 3D structure from just an image. By contrast a physical model helps to explain the structure-function-relationship, e.g. ligand binding. The very same applies to presentations or exhibitions, to e.g. leverage the physical model to make your colleagues and peers better understand your findings.

Step 1: Prepare Your Protein 3D Model for 3D Printing

First of all, you should check NIH 3D Printing exchange where you can find currently roughly 3,000 ready to print molecule models (as of Oct/2016). If your molecule of interest is not part of the collection, you can prepare your own (and make sure to post it later on NIH). If you have to generate your own, there are multiple options. An excellent instruction on how to do it with PyMol you can find here by Jessica Polka.

Many of our clients prepare their models with Chimera, therefore we thought we’ll provide you with an instruction as well.

A. Find your model on the Protein Data Base and download the model as PDB Format (gz)

B. Download and install Chimera, if you don’t have it already (Please note: the free version of the Software is only accessible to private persons and research institutes)

C. Open Chimera and open the file accordingly (File --> Open)

D. Oftentimes, there is more than one chain and sometimes the ligands are part of the model as well. If you want to remove the other chains, do the following:

  • If you want the ligands to be printed as well, we recommend doing this separately. Because of a gap between ligand and molecule, they can’t be printed in one print job.
  • So remove it for now and focus on the molecule. Select the entire chain (Select --> Chain). Go to Actions --> Atoms/Bonds --> Hide.

Step 2: Prepare the Chain for 3D-printing

First, you need to make sure the structure is strong enough and then you can apply colors if you go for a full-color print.

- Thickness of the structures: In order to adjust the sizes, select the entire chain again (Select --> Chain) and go to Tools --> Depiction --> Ribbon Style Editor. There are no fixed rules for thickness of the structures in Chimera. As a rule of thumb, the final thickness for smaller models should not be below 3 mm, and for larger ones (20 cm or more) it should be somewhere around 6 – 10 mm for the thinnest structures. In general, the thicker the better, the physical models can be rather fragile.

- Colors: If you go for a full color print, color the structures: Select --> Structure --> Secondary Structure --> Coil. Go to Actions --> Color and choose your favorite Coil color.

- Repeat the same process with Helices and Sheets.

Step 3: Export Your Model for 3D Printing

- Go to File --> Export Scene. Choose as file format STL for non-colored 3D-printing (FDM, SLS, or SLA) and VRML (.wrl, .vrml) for colored models.

- Now most models are printable, sometimes they still have some issues. To check it, you can get e.g. the free cloud-based software Netfabb (just upload, it’ll do the rest for you).

Step 4: Printing Your 3D Molecule Model

After preparing your protein model, you can finally go to printing it. Generally, there are four technologies that are often used for molecule printing:

- FDM: That’s the Ultimakers, Makerbots, Leapfrogs, Zortraxes and self-assembled 3D-printer kits that you can find in most Universities and academic Institutions nowadays. To put it short, the print is cheap, but the quality is ‘moderate’. However, for teaching purposes often sufficient.

- SLA (Stereolithography): Just like FDM, this technology requires support structures. Therefore, it is not the best use for protein models, but it is a great technology for more simple structures. Compared to FDM, the surfaces are very smooth and the print is highly accurate. We print most ligands with this technology. Probably some of your institutions have such printers already (e.g. Formlabs), if not, you can use 3D-printing services.

- SLS (Laser Sintering): With this technology you can print very complex structures because it does not require support structures. The material is (mostly) PA12 (‘Nylon’). This material is flexible when thin and rigid when thick. Therefore, you should not create your wall thicknesses too thin, because the model might collapse. This technology requires rather sophisticated machines, therefore, most institutions won’t have such equipment.

- Colorjet: As the name suggests, this technology allows full-colored prints. The material is a hardened plaster. Technically, it does not require support structures while printing, however, since the material can break, it is normally required to add some kind of permanent support structures in the molecule. Those depend very much on the geometry of the model.

Have fun preparing your own models!

There are a lot of other resources on how to create such models. Here's a list of few more:

Denis Hudrisier on YouTube (using Chimera)

Jessica Pola on (using PyMol)

Scott C. Meyer in the Journal of Chemical Education

Theabion on

For more information you can visit our homepage :)



    • Arduino Contest 2019

      Arduino Contest 2019
    • Tape Contest

      Tape Contest
    • Trash to Treasure

      Trash to Treasure



    2 years ago

    Thanks for sharing :)