A familiar frustration in molecular modeling: you find a DNA origami design that looks useful, but it is not immediately clear whether you can open it, where it came from, or what to do before using it in your own workflow. Reusing a structure can save time—but only if you keep track of its format, provenance, and intended use.
Adenita, an extension for SAMSON, lets you load and inspect several kinds of DNA nanostructure files. That makes it possible to begin with an existing design, rather than building every component from scratch. Here’s a practical way to approach that process.
1. Find a candidate structure
Repositories and shared design collections can be good starting points. For example, Nanobase includes DNA, RNA, and hybrid nanostructures, while the caDNAno Repository collects recreated caDNAno v2 designs based on published research. The Oxford Research Archive provides example caDNAno files alongside files for oxDNA simulation workflows.
You can also browse SAMSON Connect shared documents. For instance, Tom Moore’s page contains reusable DNA origami components and examples. The image below shows examples of components shared there.
2. Check the file before opening it
Adenita’s documented load options include caDNAno designs in .json format, meshes in .ply format, and Adenita files in .adnpart or .adn formats. A .ply mesh is loaded using the Daedalus algorithm. You can also load a saved Adenita component, or use a SAMSON file to create a new document.
Knowing the extension helps you choose the right expectations. A caDNAno file is a design input; an Adenita component file is intended for reuse in Adenita; and an oxDNA file belongs to a simulation workflow. They are not interchangeable just because they describe related structures. If your next step is simulation, confirm that you have the appropriate files for the tools and workflow you plan to use.
3. Import, inspect, and decide what to reuse
Install SAMSON, add Adenita from the SAMSON Marketplace, and restart SAMSON. Then open Adenita from Home > Apps or use Find everything…. Load the design through Adenita’s interface and inspect it before combining it with other components.
Adenita provides editors for creating and modifying strands, lattices, nanotubes, and wireframe structures. You can also break or connect strands, merge components, change bases, and set a scaffold sequence. These tools can help you adapt a design, but they do not replace checking whether a reused structure suits your scientific question.
4. Keep provenance and validation in the workflow
Before reusing a downloaded design, check its license, citation, and associated publication. This is especially important for recreated files: consult the original paper and validate the design before using it in a research workflow. For simulation, check that the structure is in a format your tools support, and relax or validate it when necessary before production runs.
When you are ready to save or share your work, Adenita can save a selected component as .adnpart or save Adenita-managed DNA nanostructures as .adn. It can also export sequences as CSV or export in oxDNA format for coarse-grained simulation. Saving the whole workspace as a SAMSON document is another option; note that systems not handled through Adenita are not included in an .adn save.
The useful habit is simple: treat a structure as more than a file to import. Keep its source and format attached to your decisions, inspect it in context, and only then choose whether to edit, combine, or export it.
For the full feature overview, interface details, and video tutorials, see the Adenita documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.