Working with Existing Designs: Importing Cadnano Files into Adenita

Starting a DNA origami project from scratch is often time-consuming, especially when you’re iterating on existing concepts. That’s why the ability to import pre-existing designs can be a game-changer for molecular modelers. If you’ve used Cadnano in the past and are now exploring Adenita within SAMSON, the good news is that your previous work doesn’t have to go to waste. You can import Cadnano designs directly into your Adenita workspace to continue where you left off, combine existing geometries, or move to a more visual 3D editing environment.

Why import from Cadnano?

Cadnano is a widely-used tool for designing DNA nanostructures, especially for DNA origami. However, it’s mostly a 2D interface. If you’re looking to visualize your design in 3D, refine it further, or simulate it using oxDNA, Adenita opens up new possibilities. You can also combine these designs with other molecules, such as proteins, thanks to SAMSON’s integrative environment.

How to import Cadnano designs into Adenita

Here’s a step-by-step overview of how to bring your design to life in Adenita:

  1. First, ensure you have installed SAMSON and added the Adenita Extension from the SAMSON Connect Marketplace.
  2. Launch SAMSON and locate Adenita under Home > Apps, or use the search tool Find everything….
  3. Once in Adenita, click the Load icon (Load).
  4. Select your Cadnano file in .json format (Cadnano 2.5 supported).
  5. Your design will now be visible in 3D inside the SAMSON viewport — ready to edit, export, or combine.

Adenita main interface

Next steps after import

Now that your DNA structure is loaded into Adenita, here’s what you can do:

  • Visualize with more depth: Switch between different abstraction levels — from base pair view to full 3D double-helix representation.
  • Edit directly: Use the toolbar to modify strands, break bonds, add new features like nanotubes or wireframes, or even adjust the twist angle of helices.
  • Export for simulation: Prepare your design for use with coarse-grained simulation tools like oxDNA. Export to relevant formats directly from within Adenita.
  • Combine with other molecules: Add proteins, small molecules, or other nanostructures available in the SAMSON ecosystem to simulate more complex assemblies.

Some things to keep in mind

  • Ensure your Cadnano file is compatible with version 2.5.
  • Larger designs may be limited by your hardware capabilities. Adenita allows you to import as many components as your system can handle.
  • If designs don’t appear as expected, try changing abstraction levels or checking if all strands loaded correctly. Some manual adjustments may be necessary.

Whether you’re transitioning away from Cadnano, enriching designs for simulation, or simply curious about exploring a familiar structure in an interactive 3D interface, the ability to import is both practical and empowering.

To learn more, check out the official Adenita documentation at https://documentation.samson-connect.net/tutorials/adenita/adenita/.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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