A molecular file can open successfully and still not be the right file to hand off. A structure, a trajectory, and a complete modeling session are different kinds of data—and formats that work for one may not preserve another. Before importing or exporting, ask two questions: What data do I need to carry? and Does this format support reading, writing, or both?
SAMSON’s supported-formats reference is useful for answering the second question. Its tables distinguish formats that can be read from those that can be written, and the list is explicitly non-comprehensive. Some formats are available directly; others require an extension. That distinction can save time when a file appears in a list but the action you need is not supported.
Choose the format for the job
- Continuing work inside SAMSON: consider SAM or SAMX. These native formats support many kinds of SAMSON data, including molecular structures, groups, visual models, meshes, animations, notes, and simulators. They can also embed folders and files such as scripts, PDFs, images, and data. This makes them suitable when you want to keep a broader SAMSON document together—not just exchange coordinates.
- Sharing a molecular structure: use a structure format appropriate for the receiving tool or workflow. The reference lists formats such as PDB, mmCIF/CIF, MOL2, SDF, XYZ, and others. Check the Read and Write columns rather than assuming that support is symmetrical. For example, SAMSON reads MMTF, but the table does not list MMTF writing.
- Sharing a simulation trajectory: treat the trajectory as a separate file type from the structure or topology it accompanies. SAMSON lists trajectory formats including DCD, AMBER NetCDF, TRR, XTC, and XYZ, with read/write support varying by format. Confirm what files your recipient needs to interpret the trajectory before sending it.
- Moving geometry or visuals: OBJ and glTF are listed for both reading and writing, while STL is listed for reading. SAMSON loads 3D geometries as meshes; exporting structural models, visual models, and meshes depends on the relevant model’s implemented functionality.
A quick pre-export checklist
- Identify the payload. Is this a molecular structure, a trajectory, a mesh, an image, a script, or a full working document?
- Check the direction. Verify that the selected format supports the action you need—read, write, or both.
- Check dependencies. Some formats rely on extensions. For instance, PDBQT support is associated with AutoDock Vina Extended, while GROMACS project files can be generated with GROMACS Wizard.
- Keep related files together. A trajectory may need its corresponding molecular structure or topology. The documentation specifically notes that an AMBER topology file can be used when loading AMBER NetCDF trajectories.
- Open the result before sharing. A simple round-trip check—export, then reopen the exported file—can reveal whether you chose a usable format for the intended handoff.
One useful distinction: opening a file, embedding it, and editing it are not the same operation. SAMSON can embed many kinds of files in a Document, while its Code Editor can open, edit, and save text files such as Python scripts. Embedding a file keeps it with the document; it does not mean the file’s contents have been converted into a molecular structure.
For the full format list, extension notes, and related importer/exporter information, see the SAMSON supported-formats documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.