From Published DNA Origami to a Simulation-Ready Model

A familiar frustration in molecular modeling is finding a useful DNA origami design, then discovering that the file, provenance, or intended workflow is not immediately clear. A structure may be available as a design file, a component, or simulation input—and those formats are not interchangeable. A careful import-and-check workflow can help you reuse existing work without losing track of what you have and what still needs validation.

Adenita, an extension for SAMSON, can load caDNAno designs in .json format, as well as Adenita .adnpart and .adn files. It can also load .ply meshes using the Daedalus algorithm. Once a structure is in Adenita, you can inspect and edit it, combine components, save the design, or export it—including to oxDNA format for coarse-grained simulation workflows.

Start with the source, not just the file

Before importing a design, check where it came from and what information accompanies it. Repositories such as Nanobase may provide design files, images, publication details, and, when available, oxDNA files. The oxDNA example files and the Oxford Research Archive example inputs can be useful for exploring oxDNA workflows. The community caDNAno Repository contains designs recreated from published work; its documentation recommends checking the papers and validating recreated designs before using them in research.

Keep the publication, license, and source file together with your working model. This small bit of recordkeeping makes it easier to cite the design, understand its context, and revisit decisions later. A file that opens successfully is not, by itself, evidence that the structure is suitable for a particular experiment or production simulation.

A practical import-to-export workflow

1. Identify the format. Check whether you have a caDNAno .json, Adenita .adnpart or .adn, or a mesh in .ply. If you have oxDNA files, treat them as simulation inputs rather than assuming they are one of Adenita’s listed design-import formats.
2. Open Adenita in SAMSON. Install SAMSON, add Adenita from the SAMSON Connect Marketplace, and restart SAMSON. Open Adenita through Home > Apps or Find everything….
3. Load and inspect. Use Adenita’s load function to bring a supported file into the workspace. The interface offers tools for viewing and editing strands and structures at different levels of detail. If you are combining components, remember that the number you can work with depends on your computer’s graphics card and CPU.
4. Save the right thing. Save the whole Adenita design as an .adn file, or save a selected reusable component as .adnpart. A SAMSON document saves the workspace, while Adenita’s save-all function covers DNA nanostructures handled through Adenita.
5. Choose an export for the next task. Adenita can export sequences as a CSV file or export in a format appropriate for oxDNA. After export, check that the files and structure match the requirements of the downstream tool; validate or relax the structure when necessary before production simulation.

Reuse components when starting from scratch is unnecessary

Shared documents on SAMSON Connect can provide reusable DNA origami components. For example, Tom Moore’s SAMSON Connect page includes published components and example structures, such as crossover motifs and mechanical components. These can be downloaded and opened in SAMSON. As with repository designs, check the associated license, citation, and publication information before reuse.

The useful habit is to treat import, inspection, and export as separate checkpoints: confirm the source and file type, inspect the design in the modeling environment, then select an output format for the next step. That makes it easier to spot workflow mismatches before they become simulation problems.

For more details on Adenita’s editors, file handling, and video tutorials, see the Adenita documentation page.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.