You open a molecular structure, inspect it, and prepare to send your work to a colleague. The model may be ready, but what about the script, image, paper, or data file that helped you interpret it? When those materials live only in separate folders on your computer, a handoff can become a hunt for missing context.
SAMSON documents can hold molecular content alongside embedded files and folders. That gives modelers a practical way to keep related material together when transferring a document between computers or sharing it. Here’s a straightforward workflow for assembling a more complete project document.
Start with the structure
Open a local structure with Home > File > Open, or use Ctrl+O on Windows and Linux or Cmd+O on Mac. SAMSON selects an importer based on the file format. Some importers offer parameters; the first time you use one, its settings are at their defaults, and changes are saved for later uses.
You can also fetch structures from the RCSB Protein Data Bank using the Fetch Structures app under Home > Fetch. It supports downloads in PDB, mmCIF/PDBx, and MMTF formats.
After import, check that the structure appears in both the viewport and the Document view. The Document view shows the data graph of the active document, which can contain atoms, bonds, molecules, models, simulators, and other data.
Keep supporting materials with the document
Once the structure is in place, add the files that belong with it: perhaps a script, an image, a research paper, or a folder of data. Drag files or folders into SAMSON and respond to the prompt asking whether to embed them. Alternatively, use Home > Embed files or Home > Embed folders.
Embedding matters when your work depends on more than the coordinates alone. A colleague receiving the document can have the related materials stored within it, rather than needing to locate each item separately on your computer. SAMSON documents support embedding Python scripts and folders, including Python apps, as well as other files and data.
Make sure you are working in the right document
SAMSON can have several documents open at once, but only one is active at a time. The active document is the one shown in the Document view. Before adding supporting material, confirm that the intended document is active; otherwise, you may organize your files alongside a different project than you meant to.
Switch documents from the Documents list in the top-left corner of the menu, or through Home > Documents. To start a separate project, choose Home > File > New. Keeping distinct tasks in separate documents can also make it easier to work with different molecules or copy structures between documents.
A small handoff checklist
- Open or fetch the structure you want to work on.
- Confirm it is visible in the viewport and Document view.
- Check that the correct document is active.
- Embed the files and folders that provide useful context for the project.
- Use SAMSON’s document-sharing options when you are ready to share.
The goal is simple: keep the model and its supporting materials together, so the next person has more of the context needed to understand the work. For details on opening structures, documents, and embedding files, see the SAMSON documentation on loading molecules.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.