If you’ve ever tried to switch between molecular modeling tools, you’ve likely hit the same roadblock as many others: file format compatibility. Each tool seems to speak its own language. One moment you’re saving a .PDB file, the next you’re trying to decipher what a .TRR or .SAMX file even is. This friction slows down workflows, introduces errors, and gets in the way of doing real science.
Thankfully, the latest update to the SAMSON platform makes this far less of a headache. Designed as an integrative platform for molecular design, SAMSON supports a wide array of import/export formats—covering molecular structures, trajectories, visual models, meshes, scripts, and even DNA origami.
Unified data exchange
SAMSON’s cross-format compatibility stems from its ability to read and write dozens of common file types used across disciplines: chemistry, computational biology, materials science, and nanotechnology. Whether you’re working with PDBs from the Protein Data Bank or GROMACS trajectory files like .XTC, chances are SAMSON can handle it.
Molecular structures
Here’s a snapshot of key molecular structure formats supported for both import and export:
- PDB – Widely used in structural biology
- SDF – Used for sharing chemical libraries
- MOL2 – Common in docking and modeling workflows
- CIF/mmCIF – For crystallographic data
- SMI – SMILES strings for compact molecular descriptions
Formats like .SAM and .SAMX (native SAMSON formats) allow not only storing structural data but also visual styles, simulations, notes, animations, and even embedded files like PDFs or scripts—handy for preserving entire workflows.
Molecular dynamics trajectories
For those running simulations, SAMSON supports trajectory formats that allow you to analyze molecular motion, including:
- DCD – For CHARMM, NAMD, and LAMMPS
- TRR, XTC, TNG – From the GROMACS ecosystem
- NC – AMBER NetCDF format
- XYZ – A more basic trajectory format for quick inspection
Thanks to built-in integration with the chemfiles library, SAMSON streamlines handling different trajectories without separate conversions or external scripts.
Visual outputs and scripts
SAMSON can export rendered views as PNG, JPG, BMP, or GIF images. Animations go even further: you can save them as MP4, GIF, or WEBM movies to share with others or include in presentations.
Have in-house Python scripts that analyze or manipulate data? You can open, edit, and execute .py files directly within SAMSON using its built-in Code Editor.
DNA Origami support
If you’re working on DNA nanostructures, the Adenita extension enables handling specific formats such as ADN, ADNPART, and JSON (Cadnano). Adenita even supports exporting in PLY for mesh-based DNA visualization designs.
Why this matters
This extensive format coverage means fewer interruptions. Instead of stitching together workflows from five different tools or writing format-conversion scripts, SAMSON lets you upload, analyze, simulate, design, and export—all within one unified environment. Whether you’re preparing docking input, analyzing MD trajectories, or creating a molecular animation, it saves time and reduces error risk.
Read the full supported formats list in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Learn more and download the platform at samson-connect.net.