A familiar modeling task can become unexpectedly frustrating when a file opens in one tool but not another—or when you discover that the format you need to export is not the format you can import. The first useful question is not simply “Does SAMSON support this extension?” It is: What kind of data is in the file, and do I need to read it, write it, or both?
SAMSON supports formats for molecular structures, trajectories, 3D geometry, images, animations, and more. Its supported-formats reference marks reading and writing separately. A check in the Read column does not automatically mean the format can also be written. Taking a moment to check both directions can prevent a round trip that stops at the export step.
Start with the data you have
For a molecular structure, common options in the reference include PDB, SDF, MOL2, CIF, and XYZ. Some serve different purposes: CIF includes crystallographic and macromolecular variants, while SDF supports V2000 and V3000. PDB can also be read under aliases such as ENT and VDB. If a file has an unfamiliar extension, check the listed aliases before assuming it is unsupported.
For a trajectory, identify the trajectory format separately from the structure format. SAMSON lists formats including DCD, AMBER NetCDF (NC), TRR, XTC, and XYZ. The read/write support varies by format: for example, the reference lists XTC and DCD for reading and writing, while TNG and LAMMPSTRJ are listed for reading only. AMBER topology files PARM7 and PRMTOP are listed for reading and are used when loading AMBER NetCDF trajectories. That is a useful reminder to check whether your trajectory workflow also involves a topology file.
For a mesh or geometry, SAMSON loads 3D geometries as meshes. OBJ and glTF are listed for both reading and writing; STL is listed for reading. Images are also loaded as meshes, so importing an image is not the same as adding a molecular structure. To save an image of your view, the documentation points to Capture.
Check extension requirements before planning the handoff
Most formats in the reference are available directly, but some require an extension. PDBQT is marked with ADVE: the AutoDock Vina Extended extension can generate PDBQT files and load them from its docking projects. GROMACS project files can be generated with GROMACS Wizard; the reference marks writing TOP and TPR with this extension. For DNA origami formats such as ADN and ADNPART, the listed support comes from the Adenita extension.
A practical preflight checklist is therefore: 1) identify the data category; 2) confirm the exact extension or alias; 3) check Read and Write independently; 4) note any required extension or companion topology; and 5) decide whether you need an exchange file or a SAMSON document. SAM and SAMX are SAMSON’s own formats and can contain a broad range of content, including molecular structures, visual models, meshes, animations, notes, simulators, and embedded files. They are useful to consider when the goal is to keep a SAMSON document and its associated content together, rather than exchange only a particular data type.
If a needed format is not listed, the documentation suggests contacting the SAMSON Connect Forum or developing an importer or exporter. For the full tables and format-specific notes, see the supported-formats documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.