The most fascinating final product that Jmol can produce is a 3D printed physical model. A physical model can make the abstract molecular world real and tangible.
Below is a short video that describes why the CBM considers physical models to be the cornerstone of our outreach and professional development programs.
3D Printing is a cutting edge technology that can use stacked serial planes to build physical 3-dimensional models from computer generated 3D files. Every physical protein model will go through four key steps:
When a model is built on a 3D printer, additional support struts must be added to the protein backbone to provide stability. Struts can be automatically added using the calculate struts command.
This command will only add struts to the currently selected area of a molecular structure, so you should make sure to have "all atoms" selected before adding the struts. We also suggest using a subtle color like white or gray for your struts so they are not visually overwhelming, and recommend a size of 0.75 angstroms, which compliments a backbone of 1.25 angstroms.
The basic commands used to add and format struts are similar to the commands used to format a hydrogen or disulfide bonds:
color struts gray
At times you may want to add a single strut at a precise location, perhaps to provide additional support to your design for 3D printing or to connect a small molecule that may otherwise not be connected to the protein backbone.
To do this, you will need to select only the two atoms that you want the strut to connect. Begin by hovering your mouse cursor over the two atoms in the Jmol display window to identify their atom numbers. Then select only those two atoms using the select @ command. And finally, use the connect strut command to add a strut or the connect strut delete command to remove a strut.
For example, our 1zaa.pdb zinc finger structure has three repeating motifs that are connected by two thin strands of protein backbone. This would be a good spot to add two additional struts to make the 3D printed model more sturdy:
select @810 or @621
select @860 or @1033
color strut gray
Note: The calculate struts command will add struts to any protein backbone regions selected in a molecular structure file, but does not add struts to nucleic acids (DNA and RNA) or to small molecules. If there are nucleic acids or small molecules in your model design, you will have to manually add individual struts to connect them to your protein backbone.
The CBM has created a simple checklist that can help you prepare to 3D print your protein model. The link below will open an editable PDF document with a checklist of features to review. This checklist represents the best recommended features and design sizes to use in your model design before attempting to 3D print your protein model.
Once you are happy with your model design and have reviewed the model design checklist, you are ready to export your Jmol design as an STereoLithography (.stl) File, which contains the 3d triangle mesh information used by all 3d printers.
To save a .stl file in the CBM's Jmol User Design Environment, click the orange "Save Your Design" button to expand the save menu and then click the "Save .STL File" button.
Note: Your filename must include the extension ".stl" to save properly. Also note that depending on your browser, you may need to press the "OK" button twice to initiate the save/download.
Note: .STL files exported for 3D printing can be quite large. If your browser freezes or you receive an error when attempting to export an STL file from the JUDE Web Page, click on the section below for a work-around.Java-Based Jmol: Saving Large STL Files
Start by saving your design as a Script (.spt) File in the Jmol User Design Environment. Click the orange "Save Your Design" button to expand the save menu and then click the "Save .SPT File" button.
Note that you will also need Java installed on your computer in order to run the Java-based version of Jmol. Click here to download Java for free.
Once downloaded, you will need to open the .zip file and copy the two files inside ("jmol.jar" and "jmol.bat") to your local hard drive. Double clicking on the .bat file for Windows or the .jar file for Mac will launch Jmol, initially showing an empty black screen.
Note: Some Mac users may receive an error, saying Jmol.jar is from an "Unidentified Developer". To allow your Mac to run Jmol.jar, you will need to open System Preferences > Security & Privacy, and then click the "Open Anyway" button near the bottom of the window.
Next, drag and drop your saved Script (.spt) File into the Jmol Display Window, which should then open your molecule design as it appeared in the JUDE Web Page.
Last, right click anywhere in the Jmol Display Window and select File > Export > Export STL 3D Model from the menu that appears. The Java-based version of Jmol has access to far more memory than the JUDE Web Page, and so should be able to successfully create STL files of even very large or complicated protein designs.
Once you are happy with your protein model design and have created your .stl file, you are ready to 3D print your model! There are two main options for this, each with pros and cons:
3D Print the Model Yourself
Pay Someone Else to 3D Print the Model
If you choose to 3D print your model yourself, you will most likely use a Fused Deposition Modeling (FDM) 3D Printer similar to the PRUSA Mini 3D Printer shown to the right. FDM 3D printers push plastic filament through a heated nozzle to build 3D objects one layer at a time.
Many schools have access to FDM 3D printers, and they can also be found in many public libraries, college campuses and community maker spaces. Below are two introductory videos that will provide some background on FDM 3D printing.
Using an FDM 3D printer requires experience and practice, so you should plan plenty of time into your modeling project timeline for errors, reprints and learning. While each 3D printer is unique, the overall process for FDM 3D Printing will remain the same:
3D Printing takes time and practice, so if this is your first time trying to 3D print a protein model, we highly recommend planning extra time to experiment, learn and trouble shoot. Below are a few trouble shooting resources and suggestions.
The second option for 3D printing your model is simply to pay someone else to do it for you. You can reach out to 3D printing experts in your community, such as tech departments at schools, libraries or local maker spaces, or use one of several well established online 3D print services, such as Shapeways, Craftcloud or Sculpteo
For the past several years, the CBM has predominantly used Shapeways 3D print service. Shapeways is easy to use, has very reasonable prices, and usually a quick turnaround.
Using Shapeways to 3D print your model can be quick and convenient. The overall process for 3D printing with Shapeways is:
At this point, you should be able to open molecular structure files in Jmol, manipulate their display formats and colors, focus on the specific region of the structure you think will help tell your molecular story, add sidechains, bonds and small molecules, and create .stl files to 3D print your design.
We wish you luck with your modeling projects, and would love to see photos of whatever you create! Good luck. . . and happy modeling.