A file can contain molecular data and still be the wrong file for the task at hand. A structure file describes a molecular arrangement; a trajectory records how coordinates change across frames. Some formats can be read but not written, while others depend on a SAMSON Extension. These distinctions matter when you are moving a project between tools, preparing a simulation, or trying to reopen results later.
A quick check before importing can save time: identify what kind of data you have, confirm that SAMSON can read that format, and check whether it can write the format you will need next. Here is a practical way to approach that check.
First, identify the data—not just the extension
Start by asking what the file represents:
- A molecular structure: examples include PDB, mmCIF/CIF, MOL2, SDF, GRO, and XYZ.
- A molecular trajectory: examples include DCD, XTC, TRR, TNG, and AMBER NetCDF (NC).
- A 3D mesh or geometry: OBJ and glTF are listed for both reading and writing; STL is listed for reading.
- A project or working document: SAM and SAMX are SAMSON’s native formats. They can store many kinds of SAMSON data, including structures, meshes, animations, notes, and embedded files.
This distinction is useful because a trajectory is not simply another name for a structure. A trajectory contains a sequence of coordinate frames, and SAMSON’s format reference lists trajectory support separately from molecular structure support. If you have a simulation result, check the trajectory section rather than assuming a structure-file entry covers it.
Check both directions of the workflow
“Supported” can mean different things. The documentation separates Read and Write for each format. For example, MMTF is listed as readable, with no write support shown. PSF and AMBER topology files (PARM7/PRMTOP) are also listed for reading only. By contrast, PDB and SDF are listed for both reading and writing.
That difference matters if your plan is to import a file, make changes, and export it again. Before you begin, check the output format you need—not only whether the input opens. If an output option is unavailable for a format, consider whether another listed format fits your next step, or whether an extension provides the needed functionality.
Pair trajectory data with its context
Some trajectory formats are associated with a particular simulation ecosystem. The reference lists XTC and TRR as GROMACS trajectory formats, DCD as a CHARMM, NAMD, or LAMMPS binary trajectory, and NC as AMBER NetCDF. It also notes that AMBER NetCDF trajectories are loaded with an AMBER topology file. That is a helpful reminder: a trajectory may need accompanying structural or topology information to be useful in a modeling workflow.
SAMSON uses the chemfiles library to read and write some trajectory formats. The documentation does not imply that every trajectory type has identical capabilities, so use the Read/Write entries for the specific format you have.
Look for extension requirements
Most formats in the reference are available directly, but some require an extension. The page gives examples: PDBQT functionality is associated with AutoDock Vina Extended, GROMACS project files can be generated with GROMACS Wizard, and DNA origami formats are supported by Adenita. SMILES can also be read and generated with the SMILES Manager extension. If an entry is marked with an extension note, follow that link to check the relevant tool rather than assuming the feature is built in.
A small pre-import checklist
- Is the file a structure, trajectory, mesh, image, or SAMSON document?
- Does the format appear in the relevant section of the reference?
- Do you need to read it, write it, or both?
- Does the workflow require an associated topology file or a SAMSON Extension?
- Will you need to preserve the project as a SAM or SAMX document, which can also embed files such as scripts, PDFs, and images?
These checks turn a vague “Will this open?” into a more useful question: “Can I move this data through the whole workflow I have planned?” For the complete, non-comprehensive list of supported formats and extension notes, see the SAMSON supported formats documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.