Designing and modeling DNA origami structures involves multiple tools and file formats, which can make managing and sharing your designs a bit challenging. If you work in DNA nanotechnology and are looking for a more integrated approach, SAMSON may help reduce friction in your workflow.
With the Adenita extension for SAMSON, you can read and write various DNA origami-related file formats in one place. This considerably simplifies the task of importing parts from different platforms and exporting your final models for assembly, simulation, or sharing.
What DNA origami file formats does SAMSON support?
Thanks to the Adenita extension, SAMSON can handle these file formats:
- ADN: Adenita’s native format. Ideal for preserving complete projects, including multiple components, styling, and annotations.
- ADNPART: Format for saving modular components or reused parts that can be assembled into larger structures over time.
- JSON: Includes both Cadnano files and legacy Adenita part formats. This makes it easy to bring in pre-existing structures from tools like Cadnano.
- PLY: Used for representing polygon geometries in Cadnano workflows, useful when rendering your design visualizations.
All these formats support both reading and writing, which means you can import Cadnano JSON files, edit the design in SAMSON using Adenita, and export the updated structure in the format that suits your next intended use — whether simulation or visualization.
Use Cases
Here are some common scenarios made easier with SAMSON:
- Reusing components: Save staple or scaffold modules in the ADNPART format and reuse them in other structures — no need to recreate them each time.
- Cross-tool compatibility: Import a JSON file from Cadnano to analyze, edit or convert it in SAMSON, and export to ADN format for further simulations or stylized presentations.
- Previsualization: Load PLY meshes to visualize how polygon meshes guide staple routing in certain designs.
Getting Started
If you’re working with DNA origami, all you need to begin in SAMSON is the Adenita extension. It takes only a few clicks to install from the SAMSON Connect interface, and the extension integrates directly within the modeling environment.
To dive deeper into supported file formats and additional use cases for importing and exporting data in SAMSON, visit the official documentation page: Supported formats in SAMSON
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net