Step 1) Obtaining a Molecule

If you have a molecule in mind that you wish to print then you can either download the protein data bank (PDB) file from the internet by simply searching ‘<molecule name> PDB file’. Alternatively you can draw/model the molecule you wish to print. I recommend modelling, especially within an educational environment as it is an effective tool for learning about molecular geometry.

For modelling molecules I used a software programme called ‘MoluCad’ which is a free download and very easy to use;

You simply draw atoms and bonds in and export as a ‘PDB’ file once complete. If you have opted to download a molecule rather than model one then I still suggest importing into MoluCad also (File -> Import -> Protein Data Bank File). Although PDB files can be imported directly into blender (Next step), I found in some cases the atoms are loaded without the presence of bonds, whereas importing the PDB file into MoluCAD aids in generating coordinates for the bonds. Once the PDB file has been imported or drawn simply export (File -> Export -> Protein Data Bank File) the file.

Molecule image

Step 2) Manipulating the Molecule

The next step is to manipulate the PDB file and convert to an object file (OBJ). An OBJ defines the geometry as well as other properties. To edit and convert the PDB file you can use a free software called ‘blender’. Once downloaded you will also want to download an Add-on which is called ‘Atomic Blender. This allows the user to import PDB files into Blender. Details and download link can be found here;

Once installed you can then import your PDB file (File -> Import -> Protein Data Bank File) and whilst doing so change the scaling of the molecule e.g. bond radius, scale of atom radii and distance between bonds;


When you are happy with your Molecular model, simply export as an OBJ file. (File -> Export -> Protein Data Bank File).

Step 3) Printing the Molecule

Since you are now content with the scaling of the molecule and it is saved as an OBJ file, you are now able to print the file. Depending on both the geometry and the complexity of the molecule you may have to use a support structure in order to 3D Print the molecule. In most cases, support is required. A useful software for generating support is Meshmixer which can be downloaded for free online. Not only does it generate support, but it also allows the user to delete or input extra support and thus tailor to your specific needs. It is also useful for repositioning and scaling the molecule which are important considerations when looking at appropriate support structures. Below is a link for a very useful guide into using Meshmixer;

How to -3D Printing Moleculesimg3

Once completed you choose to export as an STL and you have your finished 3D Printable Molecule.

In The Classroom

This tutorial shows you how to 3D Print your own molecules for use as manipulatives when learning the bonds and structure of different molecules. Alternatively students can investigate the structure and bonds of different molecules and design and print their own.

There are also a couple nice 3D Print designs for molecule construction sets for use in the classroom available  to download and print from Youmagine:

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