A molecular modeling session can quickly become difficult to manage: several structures are open, supporting files live in different folders, and it is no longer obvious which parts of the project belong together. That creates friction when switching tasks, revisiting work, or sharing a model with a colleague.
In SAMSON, a document can act as the organized container for a modeling task. It stores a hierarchy of nodes—not just molecular structures, but also items such as residues, atoms, groups, cameras, folders, files, Python scripts, conformations, and paths. Thinking of the document as a project workspace, rather than just a molecule on screen, can help make complex sessions easier to navigate.
Use the Document view to see what is actually in a project
The Document view displays the active document as a data graph: a hierarchical view of its contents. Open it from Interface > Document view, or use Ctrl+1 on Windows and Linux or Cmd+1 on Mac.
When a scene becomes crowded, the hierarchy gives you a place to inspect and manage its contents. You can show or hide nodes, select them, filter by node names or with Node Specification Language, and reorganize the structure by dragging and dropping nodes. Context menus and context toolbars provide actions for selected nodes.
A useful habit is to pause when a document starts feeling hard to scan and check its hierarchy. The view can help you identify which nodes are present and select the ones you want to work with. It is also where the organization of the document itself can be adjusted.
Separate tasks without losing access to your other work
You can have several documents open at once, although only one is active at a time. The active document is the one displayed in the Document view. Separate documents can be useful when working on different molecules or when you need to copy structures from one document to another.
Switch documents using the Documents list near the top-left of the menu, or through Home > Documents. On Windows and Linux, Ctrl+Tab and Ctrl+Shift+Tab move between documents; on Mac, use Cmd+Tab and Cmd+Shift+Tab. The Documents list also shows how many documents are open.
To begin a separate workspace, choose Home > File > New, or use Ctrl+N on Windows and Linux and Cmd+N on Mac. To return to a recently opened document, use Home > File > Recent. These options help keep separate tasks distinct without requiring you to close the work you are not currently viewing.
Group related nodes and keep supporting files close
Folders inside a document can group different kinds of nodes. For example, grouping nodes gives you a way to apply visibility changes to a set of molecules together, rather than handling them one by one. Create a folder from Edit > Folder, then use the document hierarchy to organize its contents.
You can also embed files and folders in a document. The supported content includes PDFs, images, data files, structure files, and scripts—in practice, any file type. Because embedded folders and files are stored within the document, the document can be self-contained and transferred between computers or shared without keeping its supporting materials in separate locations.
This is especially helpful when a model depends on more than its visible molecular structure. Keeping relevant supporting material with the document can make it easier to understand what belongs with the project when you open or share it later. For details on embedding, see the Embedding files and folders section.
A simple way to reduce project clutter
When starting a new task, consider using a separate document for it. As the project grows, use folders to group related nodes, and embed supporting files that should travel with the document. When you need to find or act on something, open the Document view and use its hierarchy, selection, visibility controls, and filters.
This approach does not replace careful file naming or scientific record-keeping. It does give you a practical way to keep molecular nodes, organization, and supporting materials together in the SAMSON workspace—and to move between distinct tasks without confusing them.
Learn more in the SAMSON Documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.