One of the most common frustrations for molecular modelers is dealing with incompatible file types across different software tools. Whether you’re switching between simulations, analyzing crystallographic data, or preparing animations, it often feels like every tool speaks its own language.
SAMSON, the integrative platform for molecular design, aims to streamline this part of your workflow by supporting a wide array of file formats across molecular structures, trajectories, 3D geometries, scripting, and more.
Start with Native SAMSON Formats
SAMSON features its own native formats: SAM (binary) and SAMX (XML), built to support extensive metadata and embedded content like molecular structures, visual models, notes, simulator data, and even whole folders.
High Compatibility with Molecular Structure Formats
SAMSON reads and writes numerous industry-standard molecular structure formats. Some highlights include:
- PDB – the widely-used Protein Data Bank format with extended read support for aliases like ENT, VDB, etc.
- CIF/mmCIF – supports both crystal and macromolecular structural data.
- MOL2, SDF, SMILES – commonly used in cheminformatics workflows.
- LAMMPS, GROMACS, AMBER – topology and coordinate files are well-supported (PRMTOP, GRO, TPR, etc.).
For advanced structural insights, formats like CSSR, MMTF, and CML are also supported.
Molecular Trajectories Are Covered Too
Don’t worry if you run simulations with various engines — SAMSON has you covered. You can read and, in many cases, write popular trajectory formats like:
- DCD – for CHARMM, NAMD, LAMMPS trajectories.
- XTC, TRR, TRJ – compressed and standard trajectory formats from GROMACS.
- NC – AMBER NetCDF-read and write support.
- XYZ, ARC, LAMMPSTRJ – for simpler or ASCII-based data workflows.
Support for 3D Models, Python Scripts, and More
You can also import and export 3D geometries as .OBJ, .glTF, or .STL (read-only). If you’re automating via code, Python scripts are fully supported and executable within SAMSON thanks to its built-in code editor.
Even image formats like PNG, JPG, and BMP are covered when capturing the viewport. Animations can be saved as GIF, MP4, or WEBM, simplifying presentation workflows.
Extensions Expand the Range
Some specialized formats, such as PDBQT for docking or ADN for DNA origami with Adenita, require installing the corresponding SAMSON Extension. These are modular add-ons available via SAMSON Connect, many of which extend SAMSON’s import/export capabilities significantly.
Unable to Find Your Format?
If a file format you use isn’t supported, you have two options:
- Contact the SAMSON team via the SAMSON Connect Forum to request it.
- Develop your own importer/exporter using the documentation on extension generation.
Being able to work seamlessly with diverse file formats is a quiet but crucial part of modern molecular modeling. With SAMSON, data compatibility becomes one less issue to worry about.
To learn more, visit the full documentation page on supported formats here: https://documentation.samson-connect.net/users/latest/supported-formats/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.