You have a molecular structure, a trajectory, or a mesh—and a deadline. The file opens in one tool but not another, or you can import it into your molecular modeling environment but cannot export it back in the same format. This is a common interoperability problem: a format name alone does not tell you whether it contains the kind of data you need, or whether your software can both read and write it.
SAMSON supports many file types, but import and export support are not always symmetrical. A useful first step is to identify what you are handling, then check the relevant format’s read and write status before planning a conversion.
Start with the data, not the extension
Ask what the file represents:
- A molecular structure: coordinates and molecular organization. Examples listed in SAMSON include PDB, SDF, MOL2, GRO, and XYZ.
- A molecular trajectory: a series of coordinate frames, often associated with a simulation. Listed examples include DCD, XTC, TRR, and AMBER NetCDF.
- A 3D geometry: a mesh or other geometric object. SAMSON lists OBJ and glTF for reading and writing, and STL for reading.
- A complete SAMSON document: SAM and SAMX can store many kinds of SAMSON data, including structures, meshes, animations, notes, and embedded files.
This distinction matters. A coordinate file and a trajectory are not interchangeable, even if both describe atom positions. Likewise, a mesh is not a molecular structure with bonds and residue information.
Check both directions
When you look up a format, treat the read and write columns as separate capabilities. For example, SAMSON documents support for reading PDB and writing PDB, while MMTF is listed for reading only. STL is also listed as readable, without write support. For trajectories, LAMMPSTRJ is listed for reading, while DCD, TRR, XTC, and AMBER NetCDF are listed for both reading and writing.
This helps prevent a frustrating workflow: importing a file successfully, making changes, and only then discovering that the same format is not available as an export option. If you need to deliver a particular format, verify write support before you begin. If it is not listed, check whether an extension provides it or choose another supported output format that suits the receiving workflow.
Look for extension-specific formats
Some formats depend on SAMSON Extensions. The documentation marks PDBQT support with AutoDock Vina Extended, and notes that the extension can load PDBQT files from its docking projects. GROMACS project files can be generated with GROMACS Wizard. DNA origami formats—including ADN, ADNPART, JSON, and PLY in the listed context—are supported by the Adenita extension.
That means a missing or unavailable option does not always indicate that the data is unusable; it may mean the relevant extension is needed. Follow the extension links in the supported-formats reference to check the associated tools.
A low-surprise workflow
- Classify the content. Decide whether you need a structure, trajectory, geometry, image, or full document.
- Check read support. Confirm that SAMSON can open the source format, and note any extension requirement or alias.
- Check write support. Confirm that the intended destination format can be produced before editing or preparing a deliverable.
- Keep the original. Work from a copy so you can return to the supplied file if a conversion does not preserve the information you need.
- Inspect the result. After loading or exporting, check that the expected content is present. A successful file operation does not, by itself, establish that every detail needed by your downstream application was retained.
For files that are not molecular data—such as scripts, PDFs, images, or other supporting materials—SAMSON documents can embed many file types. Python scripts can also be opened, edited, and saved in the Code Editor. For images, GIF files are loaded as a single image rather than as an animation; SAMSON animations can instead be saved as GIF, MP4, or WEBM movies.
The full reference is a practical checklist when you receive unfamiliar data or prepare files for collaborators. See Supported formats for the complete listed format details, read/write availability, and extension notes.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.