If you’ve ever worked with molecular data across different software tools, you probably know the struggle: incompatible file formats, conversion errors, or losing data fidelity when switching between platforms. Whether it’s importing a simulation trajectory, exporting a 3D model, or sharing molecule data with collaborators, file format compatibility is often an unexpected headache.
Enter SAMSON – the integrative molecular design platform that takes a refreshingly flexible approach to data compatibility. Let’s take a closer look at how SAMSON helps users avoid common compatibility issues by supporting a wide range of molecular file formats out of the box (and via extensions).
Common Molecular Structure Formats? Covered.
SAMSON understands that researchers and modelers come from many different workflows. That’s why it supports popular structure file formats including:
- PDB and mmCIF for macromolecules
- SDF/MOL2 for small molecules
- GRO/XYZ for molecular dynamics
- CIF for crystallographic data
- SMI (SMILES) for chemical encoding
Better yet, SAMSON can read and write most of these formats. This means you don’t have to juggle additional conversion tools—your file goes in and comes out with structure intact.
Simulation & Trajectory Support
Many modelers analyze trajectories from dynamics engines like GROMACS, AMBER, or NAMD. That’s why SAMSON incorporates support for formats used by these systems, such as:
- DCD, TRR, XTC – used by GROMACS and NAMD
- NC (NetCDF) – for AMBER trajectories
- LAMMPSTRJ – standard output for LAMMPS
Notably, SAMSON uses the chemfiles library to extend compatibility even further, offering robust read/write capabilities for many trajectory formats.
Need to Embed Your Data?
This is where SAMSON’s proprietary file formats, SAM and SAMX, come in handy. These formats don’t just store structures – they can embed scripts, images, notes, and entire folders. Perfect for sharing a whole project in a single file with colleagues.
Going Beyond Molecules
SAMSON isn’t just about atoms and bonds. It also allows import/export of:
- 3D geometric files like
OBJ,STL, andglTF - Image formats including
PNG,JPG, andBMP - Animation exports in
MP4,WEBM, or animatedGIF - Python scripts (
*.py) for executing workflows within SAMSON
Have something more specialized? With the Extension system, you can load support for formats like PDBQT (AutoDock Vina extended), or DNA origami formats via Adenita extensions.
Still Missing a Format?
If SAMSON doesn’t natively support a format you use, there are two practical solutions:
- Use the SAMSON Forum to request support.
- Develop your own importer or exporter via the Extension Generator.
This development flexibility—in code or clicks—helps keep SAMSON adaptable to your evolving workflow.
Visual Overview of Supported Formats
To explore the full list of supported formats and additional details, visit the SAMSON Supported Formats documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.