A molecular structure can look complete on one computer and become confusing on another. The model may load, but a useful project can also depend on scripts, images, papers, data files, or folders kept elsewhere. When those materials are scattered across a desktop or shared drive, handing the work to a colleague—or returning to it months later—can turn into a search for missing pieces.
SAMSON documents offer a practical way to keep related materials together: embed files and folders in the document that contains your molecular work. The result is a document that can carry its embedded contents when you transfer or share it.
Think of the document as a project container
A SAMSON document stores information about its molecular content, including atoms, bonds, molecules, models, and other nodes. It can also hold files and folders through Universal File Embedding. That means the document can include more than the structure itself: for example, a research paper you refer to, images used to interpret a system, a data folder, or Python scripts associated with your work.
This is especially useful when the scientific context matters as much as the coordinates. Instead of asking a collaborator to reconstruct which supporting files belong with which model, you can place those materials in the same document.
A simple workflow for keeping related files together
- Open or create the document for your work. A loaded or created molecule is added to the active document. If you want a separate project, create a new document using Home > File > New.
- Gather the supporting materials. Decide which files or folders another person would need to understand or continue the work. This might include scripts, data, images, or papers.
- Embed them. 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.
- Save and share the document. The embedded files and folders are stored within the document, making it self-contained with respect to those items. You can then transfer it between computers or share it through SAMSON Connect.
Keep the project easy to navigate
Before embedding a large collection, take a moment to identify what is genuinely part of the project. A concise set of relevant materials is easier for someone else to understand than a folder of unrelated downloads. Clear filenames and a sensible folder structure also help collaborators locate the right script, image, or dataset after opening the document.
It can help to keep separate projects in separate documents. SAMSON lets you have several documents open, while only one is active at a time. The active document is the one shown in the Document view, so check which document is selected before embedding files. You can switch documents from the Documents list or through Home > Documents.
One useful distinction: opening a molecular file and embedding supporting materials are different steps. Use Home > File > Open to load a structure; SAMSON selects an appropriate importer based on the file format. Use the embedding options when you want files or folders stored inside the document. If an importer presents parameters, review them before confirming—the settings can be retained for later uses.
Embedding makes a document more portable, but it does not replace thoughtful project organization. Include the materials needed to make the work understandable, and tell collaborators what they are looking at. For more details on opening structures, documents, and embedding files, see the SAMSON loading molecules documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.