A molecular file can open successfully and still be the wrong choice for the next step in your workflow. You might need to share a structure with a colleague, inspect a molecular-dynamics trajectory, preserve a complete working document, or export a mesh for another tool. The important question is not just “Can SAMSON read this?” It is also “Can it write it, and does this format suit what I need to carry forward?”
A useful first check is the difference between Read and Write. A format listed as readable can be imported into SAMSON; that does not necessarily mean SAMSON can export it. For example, MMTF is listed for reading but not writing, while PDB and SDF are listed for both. If you need to send a file back out, check the Write column before building your handoff around a particular format.
Choose by what you need to preserve
If you are saving a SAMSON working document, consider the native SAM or SAMX formats. The documentation describes these as supporting a broad range of SAMSON data, including molecular structures, groups, visual models, meshes, animations, notes, and simulators. They can also contain folders and other files, such as scripts, PDFs, and images. That makes them a practical choice when the goal is to retain a richer SAMSON document rather than share only a molecular structure.
For exchange with other molecular tools, choose an interchange format that matches the type of data you are moving. The supported structure formats include PDB, mmCIF, MOL2, SDF, and XYZ, among others. These are not all interchangeable in purpose: a simple coordinate format such as XYZ is different from a chemical table format such as SDF, and a molecular structure file is not the same thing as a trajectory.
| What you are handling | Formats to check | Useful detail |
|---|---|---|
| A molecular structure | PDB, mmCIF, MOL2, SDF, XYZ | Check Read and Write support for your chosen format. PDB and SDF are listed for both. |
| A molecular-dynamics trajectory | DCD, NC, TRR, XTC, PDB, XYZ | Trajectory support varies: for example, XTC is listed for reading and writing, while TRJ is listed for reading only. |
| A SAMSON project with additional document content | SAM, SAMX | These formats can store a wider range of SAMSON data and embedded files. |
| A 3D mesh or geometry | OBJ, glTF, STL | OBJ and glTF are listed for both reading and writing; STL is listed for reading. |
Keep trajectories distinct from structures
A trajectory is a sequence of coordinates, not simply another name for a structure file. SAMSON lists formats such as DCD, AMBER NetCDF (NC), GROMACS TRR and XTC, and LAMMPS trajectory files. Their read/write support differs. For instance, LAMMPSTRJ is listed as readable but not writable, whereas DCD, NC, TRR, and XTC are listed for both. Some trajectory formats also depend on a corresponding structure or topology file, so check what files your workflow requires before sharing a trajectory on its own.
Look for extension-dependent formats
Not every listed format is available in the same way. Some require an extension. The documentation notes that PDBQT support is associated with AutoDock Vina Extended, and that GROMACS project files can be generated with GROMACS Wizard. DNA-origami formats are supported by Adenita. When a format matters to your project, verify whether the relevant extension is needed and whether it supports the direction you need—importing, exporting, or both.
A quick handoff checklist
- Identify what you are transferring: a structure, trajectory, mesh, image, or full SAMSON document.
- Check the format’s Read and Write support separately.
- Confirm whether an extension is required, especially for specialized formats.
- If you are handing off a trajectory, check whether the recipient also needs a structure or topology file.
- For a project that relies on SAMSON-specific content, consider saving a SAM or SAMX copy alongside any interchange file.
This small check can prevent a common handoff problem: having a file that opens, but not the kind of file—or the export path—you actually need. For the complete format list and additional 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.