Anyone who has worked with molecular modeling knows the frustration of incompatible file formats. You might receive data in PDB format from a colleague, simulate a system in LAMMPS which outputs a DAT file, or need to visualize a CIF crystal structure. The tools you use have to speak the language of science — and that means supporting a wide range of formats.
SAMSON, the integrative platform for molecular design, provides a practical approach to this common pain: it supports a large and diverse list of import/export formats across different molecular modeling domains. This includes structural data, simulation trajectories, 3D geometries, visualization assets, and even scripting files.
Why Format Compatibility Matters
When working with multiple tools or collaborating across labs, models and simulations often need to move through different software platforms. Each one has its own preferred file types: PDB for structural biology, XTC and TNG for GROMACS, PRMTOP for AMBER, and so on.
If your primary tool can’t read what your collaborator sends, you spend valuable time converting formats manually or re-running simulations. This isn’t just tedious — it can lead to data loss or misinterpretation.
How SAMSON Helps
The documentation lists a variety of file types that SAMSON can load or export. Here’s a quick overview of supported categories and some examples:
Structural Formats
- PDB (Protein Data Bank) files are fully readable and writable.
- CIF/mmCIF, MOL2, and SDF formats are supported, covering both crystal structures and small molecules.
- LAMMPS, GROMACS (GRO, TOP, TPR), and AMBER (PRMTOP, NETCDF) are readable for those working with MD simulation tools.
- SAMSON also supports newer formats like MMTF (Macromolecular Transmission Format).
Trajectory Formats
- DCD, XTC, TRR, and NC files can be opened and, when possible, written back. These are essential for analyzing long MD simulations.
- SAMSON internally uses the chemfiles library to manage various trajectory file types.
Meshes and 3D Geometries
- SAMSON imports and exports formats like OBJ, STL, and glTF, offering compatibility with external visualization tools or 3D printing.
Images and Animations
- You can export high-quality images to PNG, JPG, or BMP via the Capture tool.
- Animations can be saved as GIF, MP4, or WEBM.
Python Scripts
- Python files (.py) can be opened, edited, and executed directly inside SAMSON thanks to its built-in Code Editor.
One Format to Rule Them All?
Interestingly, SAMSON also introduces its own formats: SAM (binary) and SAMX (XML), which can store complex data like visual models, simulators, and embedded files (e.g., scripts, PDFs, images). These formats are ideal for sharing complete molecular design projects.
Adding More Formats
If you come across a file type SAMSON doesn’t support, you have two options:
- Request the format via the SAMSON Connect Forum.
- Develop your own importer/exporter via the Extension SDK.
By addressing one of the most common bottlenecks in collaborative modeling workflows — data compatibility — SAMSON enables smoother integrations between experimental and computational tools.
To learn more, visit the full list of supported formats in the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.