A molecular modeling session can accumulate more than molecular structures. It may also involve scripts, reference images, PDFs, conformations, paths, and other supporting material. When those pieces are scattered across folders or mixed into one crowded view, it becomes harder to tell what belongs together—and easier to lose context when moving a project to another computer.
SAMSON documents offer a practical way to keep that context organized. A document is a hierarchy of nodes: it can contain structural nodes such as molecules, residues, atoms, and groups, as well as cameras, folders, files, Python scripts, conformations, paths, and more. Thinking of the document as a project workspace—not just a place to display a molecule—can make everyday work clearer.
Start with the Document view
The Document view displays the active document as a data graph. Open it with Interface > Document view, or use Ctrl+1 on Windows and Linux and Cmd+1 on Mac. From here, you can inspect the hierarchy, show or hide nodes, select them, filter by names or Node Specification Language, and reorganize nodes by dragging and dropping.
That hierarchy can help answer simple but important questions: Which nodes belong to this molecule? Where are the supporting files? Have I hidden a structure, or is it simply elsewhere in the document? A useful habit is to check the Document view when a project starts to feel difficult to navigate, rather than relying only on what is currently visible in the molecular view.
Use folders to make groups easier to manage
Folders let you group different types of nodes and apply operations to sets of molecules. For example, if you want to show or hide a set of molecules together, placing them in a folder can make that task more straightforward. Create a folder with Edit > Folder, then use the document hierarchy to keep related items together.
Folder names can also serve as lightweight signposts for your future self or a collaborator. Consider naming groups according to their role in the project—such as a set of structures or supporting materials—so the document is easier to interpret. This is an organizational suggestion, not a required naming system; the useful structure is the one that makes the contents clear to the people using the document.
Keep supporting files with the project
A document can contain embedded files, including PDFs, images, data files, structure files, and scripts. It can also contain folders with files. Because these items are stored within the document, the document can be self-contained, making it easier to transfer between computers or share without separately gathering every related file.
This is especially useful when a file explains or supports the molecular work: a reference image, a script, or a data file can travel with the document rather than remaining an unexplained item in a separate directory. Before sharing, consider what another person will need to understand the project, and embed those materials where appropriate. For details on embedding, see Embedding files and folders.
Keep separate tasks separate
You 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. This makes it possible to work with different molecules in separate documents or copy structures from one document to another without treating every task as one large workspace.
Switch documents from the Documents list in the top-left corner of the menu, or through Home > Documents. The interface also shows how many documents are open. To start a fresh workspace, choose Home > File > New; to return to a recently opened document, use Home > File > Recent.
A small routine can prevent a lot of project friction: keep distinct tasks in distinct documents, arrange related nodes in folders, and embed the files that provide necessary context. When it is time to move or share the work, the document hierarchy can help you check what is included and how it is arranged.
For the complete guide, see the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.