A file that opens is not always a file that contains everything you need. Molecular structures, simulation trajectories, meshes, and visual assets are different kinds of data, and a format that works for one may not work for another. Export support can also differ from import support. Checking these details before moving between tools can save time and help prevent avoidable gaps in a modeling workflow.
SAMSON supports a broad range of formats, but the useful question is not simply, “Is this extension supported?” It is: Can I read this specific kind of data, and can I write it back out in the format my next step needs? The supported-formats reference is organized around that distinction.
First, identify what the file represents
Start by sorting your file into a data category. A coordinate file for a molecular structure is not the same thing as a trajectory containing many time steps. A mesh is a 3D geometry, while an image may be loaded as a mesh for viewing. A video is an output for presenting an animation. These categories have different format options in SAMSON.
- Structures: Examples include PDB, mmCIF/CIF, MOL2, SDF, GRO, and XYZ.
- Trajectories: Examples include DCD, AMBER NetCDF (NC), TRR, XTC, and PDB.
- 3D geometries: OBJ and glTF can be read and written; STL is listed for reading.
- Images and movies: BMP, JPG, and PNG can be read and written. GIF can be read as a single image, while GIF, MP4, and WEBM can be written as movies.
This quick classification helps avoid a common mismatch: choosing a format based on its name without checking whether it represents the data you intend to move.
Check reading and writing separately
Format support is not necessarily symmetrical. In the reference table, a check under Read means SAMSON can import that format; a check under Write means it can export it. Some formats are read-only in the listed workflow. For example, MMTF and PSF are listed for reading as molecular structures, while STL is listed for reading as a 3D geometry. If a format is absent from the Write column, do not assume you can export to it.
There are also entries that depend on extensions. PDBQT support is associated with AutoDock Vina Extended, and GROMACS project files can be generated with GROMACS Wizard. The table marks these cases so you can distinguish built-in format handling from extension-provided workflows. Check the linked extension information when a file type is marked with a note rather than a standard read or write check.
Choose a structure format for the next step
PDB is a familiar option and is listed for both reading and writing as a structure format. For macromolecular crystallographic data, the reference identifies CIF and its aliases PDBx and mmCIF; writing is specified as PDBx/mmCIF. CIF for crystal structures is handled through the Crystal Creator App. That distinction matters: the same short extension can be associated with different use cases, so consider what produced the file and which application must receive it next.
Other common options include SDF, which supports V2000 and V3000 and can be read under aliases such as MOL and SD, and SMILES, which can be read and generated with the SMILES Manager extension. These formats serve different purposes. When you are unsure which representation your downstream tool expects, check its import requirements before exporting.
Keep trajectories and their structures distinct
A trajectory generally supplies changing coordinates, while a structure file describes a molecular model. SAMSON lists several trajectory formats as readable and writable, including DCD, AMBER NetCDF, PDB, TRR, and XTC. Other listed trajectory formats, such as TNG and LAMMPSTRJ, are read-only in this table. Some trajectory workflows may also need a topology or structure file alongside the trajectory; for example, the documentation notes that an AMBER topology file is used when loading AMBER NetCDF trajectories.
Before loading a trajectory, make sure you have identified the associated structure or topology files required by the format and workflow. Keeping these files together and clearly named makes it easier to reopen the system later and reduces confusion about which model belongs with which coordinate series.
A simple pre-export check
- Identify whether your data is a structure, trajectory, mesh, image, script, or movie.
- Confirm that SAMSON can read the source format and write the format required by your next tool.
- Check whether the format depends on an extension, and install or consult that extension if needed.
- For trajectories, keep the associated structure or topology information available.
- After exporting, reopen the result or verify it in the receiving application before relying on it.
The last check is a practical safeguard, not a guarantee that every format preserves every piece of information. Molecular workflows often involve several file types, and different tools may interpret or store data differently. Keeping the original files until the handoff is verified gives you a straightforward way back if something is missing.
SAMSON also has native SAM and SAMX formats for saving a wide range of document content, including molecular structures, visual models, meshes, animations, notes, and embedded files. For the full list of formats and extension notes, see the SAMSON supported formats reference.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.