A molecular structure rarely travels alone. A project may depend on scripts, images, data files, or other materials that explain or support the model. When these items are scattered across folders, sharing the structure can leave someone else with an incomplete project—or leave you searching for files when you return to it later.
In SAMSON, a document can hold more than molecular models. It can also contain files and folders, including Python scripts and other research materials. Embedding related content in the same document gives you a practical way to keep project materials together when you transfer or share the document.
Think in terms of the whole project
Before sharing a molecular model, ask what a collaborator would need alongside the structure to understand or continue working with it. That might include a script, an image, or a folder of supporting data. The structure alone may be enough for some tasks; for others, those companion files are part of the working context.
SAMSON documents store information about atoms, bonds, molecules, models, simulators, and more. The Document view shows the data graph of the active document, giving you a place to see the contents you are working with. You can open it through Interface > Document view.
You can have several documents open, but only one is active at a time. This matters when organizing a project: check which document is active before adding files, especially if you are switching between different molecules or tasks. Use the Documents list near the top-left of the menu, or choose Home > Documents, to switch documents. To start with an empty document, choose Home > File > New.
Embed the supporting material
To add files or folders to a document, drag and drop them into SAMSON. You will be asked whether you want to embed them. You can also use Home > Embed files or Home > Embed folders.
Embedding is useful when you want the related material stored within the document rather than left as a separate item on your computer. The documentation describes this as making the document self-contained, so documents can be transferred between computers and shared. It is a straightforward way to reduce the chance that a recipient receives the molecular model but not the files you intended to accompany it.
As a simple workflow, first open or create the document for the molecule you are working on. Then add the supporting files and folders that belong with that work, and confirm that you are adding them to the intended active document. When you later share or transfer the document, its embedded contents travel with it.
Keep importing and embedding distinct
Opening a molecular structure and embedding project materials solve different problems. Use Home > File > Open to load a local structure; SAMSON selects an importer based on the file format. Some importers may show parameters, which are set to defaults the first time and saved for later use if you change them. To retrieve structures from the RCSB Protein Data Bank, the Fetch Structures app is available through Home > Fetch.
After loading the structure, add any companion files that should remain part of the same project. This distinction helps keep the workflow clear: import the model you want to work with, then embed materials that should travel with the document. Not every file on your computer needs to be included—choose the items relevant to the project and its intended recipient.
For details on loading structures, documents, and embedding files and folders, see the SAMSON documentation on loading molecules.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.