Introduction: Automated 3D Printing of Virus Models From Databases

By Acheron
About: My name is Aaron Berliner. I studied bioengineering, control theory, optimization theory, synthetic biology, systems biology, nanotechnology, artificial neural networks, and some microelectromechanical system …

The products of virology, although crucial in molecular biology and medicine, can be esoteric and difficult to appreciate. In order to provide a better way for the populace to understand the objects the objects of study in virology, viruses models are often created, modified, and 3D printed. This guide will help you download a virus (or other protein) file from various databases, prepare it for 3D printing, and order your 3D printed model!

Step 1: Get the Software You Need

This Instructable requires the following software for easily downloading virus files and 3D printing those files through a service like Shapeways.

UCSF Chimera

  1. Navigate to the UCSF Chimera download page
  2. Download and install the package specific to your OS

Autodesk Meshmixer

  1. Navigate to the Autodesk Meshmixer homepage
  2. Download and install the package specific to your OS

Step 2: Get a Virus

There are many ways to download virus map or .STL data. Let's start with a simple example of just using the UCSF Chimera tool to obtain the data.

  1. Open up the newly installed UCSF Chimera application.
  2. Navigate to File and select Fetch by ID.
  3. Once the Fetch by ID window is open, select the protein file database of your choosing. In this case we will be using the Electron Microscopy Data Bank (EMDB) database and printing the lemon-shaped virus His1 (EMDB-6222) Note that the data needs to be downloaded which can take some time. Be Patient.
  4. Load the data! Explore the downloaded MAP file!
  5. Navigate to File and select Export Scene.
  6. Navigate to a directory of your choosing. Then browse the File type tab and select STL[.stl].

You have now downloaded a virus file from the database and exported it for mesh editing!

Step 3: Get Your Virus Ready for Printing

  1. Open up the newly installed Autodesk Meshmixer
  2. Navigate to and click on the Import icon.
  3. Navigate to and import your previously exported STL file.
  4. Note that the scale is way off by realizing that the file extends beyond the boundaries of the print bed. This is because the virus in Chimera recognizes the units of nanometers. When the virus map is converted to a STL file, the units are lost in translation. When Meshmixer imports the STL, the program assumes either millimeters (default) or inches. Thus, a conversion is needed!
  5. Navigate to and select the Edit icon on the left of the application.
  6. Navigate to and select the Transform option in the Edit tab.
  7. Navigate to and edit the X scale data. We will be changing 1 to 0.1 which will scale down the STL by a power of 10.

Attachments

Step 4: 3D Print That Virus

  1. Once you are satisfied with your virus model, navigate to and select Print on the left of the application.
  2. Navigate to and select the printer type (in this figure it was Stratasys Objet Connex and select Shapeways
  3. Navigate to and select Repair Model. This will repair broken regions of the STL with specific care to mend regions that would be a problem for the printing type of interest. Generally, this repairs non-manifold geometry errors that arise during conversions between file and geometry types.
  4. Select your material of interest. Shapeways has a variety of choices of material and printing specifics. Play around!
  5. Navigate to and select Review Cart & Order
  6. Navigate to and select Order in the Meshmixer Shopping Cart window.
  7. You will be brought to the Shapeways website. You can log in with a facebook ID (that is what I usually do). From there, you can play with and finalize the order for your print.
  8. Choose from the many options, order your print, then wait a couple days for the prints to show up!
  9. Enjoy!