jMol Tutorial

3D Printers in the Biology Classroom
3D Printers in the Biology Classroom

Prior to completing any of the steps below, please right click on the Jmol window to the right, and select 'Console.'

Loading Molecules Into Jmol

Loading Simple Molecules

Jmol possesses the ability to display a wide variety of simple molecules in three dimensions. Try loading a simple molecule, like glucose, by inserting the following command into Jmol; load$glucose. If this fails, double check your syntax and spelling, and then try again.

Please note that the simple molecules added in this manner will likely work best for most desktop 3D printers. With the right modifications, however, some printers can handle much more complex molecules.

Loading More Complex Molecules

Jmol can also help you prepare these more complex molecules. To load these molecules into Jmol, however, you will need to follow a slightly modified process. This process requires you to find a .pdb file for the molecule you wish to manipulate. This can be done by visiting the following website and searching for your desired macromolecule: Once you have found the protein you would like, copy the four letter sequence by which it is labeled, and insert the following command into Jmol: load=four letter sequence of molecule.

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Protein Data Bank entry for hemoglobin

For example, one of the PDB entries for hemoglobin has the four letter code of 1BUW. In order to view this molecule in Jmol, enter the command 'load=1BUW' into Jmol.

An Alternative Method of Loading Molecules

One final method you can use to get Jmol to display a molecule is to utilize the molecules SMILES code. SMILES is a notation which describes the three dimensional structure of a given molecule. To get Jmol to display a molecule based on the SMILES code, you first need to find the molecules unique code. The easiest way to do this is to look at the information box found on the molecules Wikipedia page.

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SMILES notation for glucose

Once you have done this, copy the SMILES code, and insert it into Jmol console editor using the following command: load$smilescode.

Modifying Your Jmol Molecule to Maximize the Chances of 3D Printing Success

The initial view of the molecule loaded into Jmol will require some modification prior to 3D printing. The extent of this modification will vary somewhat based on the complexity of your molecule, and any considerations you have in regards to the story you wish to tell.

Preparing Small, Simple Molecules

If you are working with a relatively simple molecule, the following commands will likely suffice as the suggested modifications.


Preparing Complex Molecules

More complex molecules, such as the majority of proteins, will likely not print well with the above commands. Additionally, the majority of desktop 3D printers will struggle to print more complex molecules because the molecules have a significant amount of 'empty' space that requires support filling when 3D printing. If you wish to test your skill, in addition to the power of your 3D printer, however, then I recommend you start by strongly considering the story you wish the model to tell.

Many proteins tell an interesting story based simply on their backbone structure. If you wish to do this, use the following command sequence:
backbone only
backbone 3.0
calculate struts
struts 2.0
calculate hbonds hbonds 2.0

If instead you wish to print a molecule in space fill format, then the command sequence below should work well.
spacefill only
spacefill 3.0
calculate struts
struts 2.0
calculate hbonds hbonds 2.0

Notice that these larger proteins will likely also require additional support in the form of 'struts' for long term stability. This command was added was added using the following command sequence: calculate struts; struts 2.0.

Finally, you can get really crazy and build a model that tells the exact story you want to share. This will likely take a fair bit of problem solving and frustration, especially at first. Use the resources available at the link below to help you struggle productively, and don't be afraid to contact me at


Exporting Your Molecule for 3D Printing

Once you have designed the molecule to the suggested, or your preferred, specifications, you can use Jmol to export an .stl file. In order to do this, right click on the Jmol window, select 'File' -> 'Export' -> 'Export STL 3D Model.' You will eventually load this .stl file into a splicing program, such as Cura, to prepare the print.

Last modified: Thursday, 7 September 2017, 3:59 PM