Transferring data between different tools and formats is one of the most common pain points in molecular modeling workflows. Whether you’re importing a complex structure from a crystallography database, exporting atomic trajectories after a long simulation, or working with DNA origami platforms, format compatibility often gets in the way.
SAMSON, the integrative platform for molecular design, addresses this challenge by supporting a wide variety of file formats out of the box—and more via extensions. Here’s a detailed look at the formats you can import and export in SAMSON to make your workflow smoother, faster, and more interoperable.
⭐ Native SAMSON formats
SAMSON supports its own formats—SAM (binary) and SAMX (XML)—to save an entire project, including molecules, simulations, animations, meshes, and even embedded scripts or PDFs. These formats serve as all-in-one containers for everything you create in SAMSON.
🧬 Molecular structure formats
SAMSON supports many formats used in structural biology, quantum chemistry, and material science:
- PDB, mmCIF: For protein and macromolecular structures (including aliases like PDBx, ENT, VDB).
- SDF, MOL2, SMI: For small molecules, ligand design, and cheminformatics.
- GRO, LMP, PSF, TOP, TPR: For GROMACS, LAMMPS, and CHARMM data.
- CML, MMTF, XYZ, CSSR: Diverse formats across quantum chemistry and crystallography.
Many formats are both readable and writable, which means full-cycle modeling is possible inside SAMSON.
📽 Molecular trajectory formats
Need to load trajectories from your MD simulations? SAMSON supports common formats such as:
- DCD: Used by CHARMM, NAMD, LAMMPS
- TRR, XTC, TNG: GROMACS formats
- NC: AMBER NetCDF trajectories
- XYZ, ARC, LAMMPSTRJ: General coordinate formats
Support for these formats is made possible by SAMSON’s integration with the chemfiles library.
🧱 3D geometries and meshes
SAMSON allows users to import and export 3D meshes using:
- OBJ: Wavefront geometry
- glTF: Efficient transmission format
- STL: For 3D printing and geometry modeling (read only)
Meshes can represent molecules, visual models, or user-defined graphics.
📜 Scripts and documents
Python scripting is supported directly in SAMSON. Users can read, write, and execute Python files (.py) using the built-in Code Editor. This enhances reproducibility and automation in your modeling workflows.
🖼 Images and capturing
Use SAMSON’s Capture feature to export static views of your models in formats such as PNG, JPG, and BMP. Supported image imports include GIF, PBM, XBM, and others.
🎬 Animation exports
SAMSON lets you record animations and export them as GIF, MP4, or WEBM. This makes it easy to present structural transitions, trajectories, or conformational scanning results in talks or publications.
🧬 DNA origami modeling
Working with DNA origami? The Adenita extension adds support for:
- ADN, ADNPART: Adenita project and part formats
- JSON: Cadnano schemes
- PLY: Mesh structures
These specialized formats enable complex nanoscale design directly within SAMSON.
🧩 Can’t find your format?
If you work with a custom format that is not currently supported, SAMSON lets you develop your own importers and exporters through its extension architecture. Alternatively, you can also submit a request on the official SAMSON forum.
For the full list and more details, please visit the SAMSON supported formats documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download it today at https://www.samson-connect.net.