A molecular structure can look complete in the viewport while the work around it still lives elsewhere: a reference image in Downloads, a script in a project folder, or notes on another computer. That split creates a familiar handoff problem: the recipient gets the molecule, but not the material needed to understand or continue the work.
SAMSON documents offer a practical way to keep related material together. A document stores the data graph for the active project—including atoms, bonds, molecules, models, and other nodes—and can also embed files and folders. The key is to distinguish opening a structure from including the project’s supporting files.
Start with the structure
Open a local structure with Home > File > Open, or use Ctrl+O on Windows and Linux and Cmd+O on Mac. SAMSON selects an appropriate importer based on the file format. Some importers present settings before loading; their default parameters are used the first time, and changes are saved for the next use. Confirm the dialog with OK or Enter.
If you need a structure from the RCSB Protein Data Bank, the Fetch Structures app, available via Home > Fetch, can download files in PDB, mmCIF/PDBx, and MMTF formats. If a local file’s format is not supported by the available importers, check the supported-formats list or look for another importer in the SAMSON Connect Marketplace.
After import, find the structure in the Document view and viewport. The Document view is more than a list of open files: it shows the data graph of the active document. This is a useful first check that the structure has loaded into the document you intend to work on.
Keep the context with the molecule
To include supporting material, drag files or folders into SAMSON and choose to embed them when prompted. Alternatively, use Home > Embed files or Home > Embed folders. Documents can contain Python scripts, files, folders, research papers, images, data, and other material—not just molecular models.
Embedding stores those files and folders within the document, making it self-contained for transfer between computers and for sharing. This can help avoid the common mismatch between a structure and the references or project materials someone needs alongside it. Before sharing, consider which files are genuinely part of the work and add those to the document; embedding does not replace the need to explain what the materials are or how they relate to the model.
Use documents to keep tasks separate
You can have several documents open, but only one is active at a time. Switch between them from the Documents list or via Home > Documents. Separate documents can be useful when working on different molecules or when you need to copy structures from one document to another. Create a fresh document with Home > File > New, and use Home > File > Recent to return to recently opened files or documents.
A simple handoff habit: confirm the right document is active, check that the structure appears in the Document view, and embed the supporting files and folders that should travel with it. Then share the document rather than assuming a separate folder will accompany it.
For details on opening structures, documents, and embedding files, see the Loading molecules documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.