A familiar frustration in molecular modeling: a file opens, but not in the way you expected. Perhaps it contains coordinates but no trajectory, or the application can read a format but cannot write it back. Before converting files—or trying one format after another—it helps to separate three questions: what kind of data is in the file, does SAMSON read it, and can SAMSON write it?
The supported-formats reference lists these capabilities separately. A check in the Read column does not mean the same format is available for export. And some entries depend on an extension, rather than being ready to use immediately. Here’s a practical way to navigate the common handoff cases.
First, identify the data you’re moving
A molecular structure and a molecular trajectory are different kinds of data, even when both use a familiar extension such as PDB or XYZ. The documentation lists formats by data category, so start with the section that matches your file: molecular structures, molecular trajectories, 3D geometries, images, or another category.
For example, PDB appears under both molecular structures and molecular trajectories, with read and write support listed for each. XYZ is also listed in both categories, but its structure entry and trajectory entry describe different uses. The extension alone may not tell you what information the file contains; check the file’s origin and intended use as well.
Choose an exchange format by the job
- Moving a molecular structure: PDB is listed for reading and writing. SDF supports V2000 and V3000, with MOL and SD listed as read aliases. MOL2 is also listed for reading and writing.
- Moving a trajectory: DCD, AMBER NetCDF (NC), PDB, TRR, XTC, and XYZ are among the listed read-and-write options. Other trajectory formats, including TNG and LAMMPSTRJ, are listed as readable but not writable.
- Moving a mesh or geometry: OBJ and glTF are listed for reading and writing; STL is listed for reading.
- Keeping a SAMSON document together: SAM and SAMX are SAMSON’s own formats. They can store a broad range of SAMSON data, including molecular structures, visual models, meshes, animations, notes, and embedded files.
That last distinction matters. A format intended to exchange molecular coordinates is not necessarily a container for the wider state of a project. If your handoff needs to retain SAMSON-specific content, SAM or SAMX may be more suitable than a structure-only format.
Watch for companion files and extensions
Some data needs context from another file. The reference notes that an AMBER NetCDF trajectory can be loaded with an AMBER topology file, listed as PARM7 or PRMTOP. If you have a trajectory but it does not load as expected, check whether the matching topology is also available.
Extension-dependent support is another common source of confusion. PDBQT read and write are associated with the AutoDock Vina Extended extension. GROMACS project files can be generated with GROMACS Wizard; the table marks TOP and TPR writing with that extension. The CIF entry also distinguishes crystal-structure CIF support through Crystal Creator App from macromolecular mmCIF/PDBx support.
A quick preflight checklist
- Identify whether the file contains a structure, trajectory, geometry, or something else.
- Check the matching category—not just the extension name.
- Confirm the specific direction you need: read, write, or both.
- Look for notes about companion files, aliases, and required extensions.
- For a project handoff, decide whether you need coordinates alone or a SAMSON document with additional content.
This small check can prevent a lot of trial-and-error, especially when a file appears supported but the needed export path or extension is different. For the complete format list and its notes, see the SAMSON supported formats reference.
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