A molecular modeling session can quickly become a collection of disconnected pieces: structures in one place, scripts in another, reference images in a folder, and several alternative molecules open at once. When you return to the work—or share it with a colleague—the challenge is not only finding the right structure. It is understanding how the pieces fit together.
In SAMSON, a document is a hierarchy of nodes that can hold structural data, such as molecules, residues, atoms, and groups, alongside cameras, folders, files, scripts, conformations, paths, and other nodes. Thinking of the document as a workspace for related project material can make it easier to keep a modeling task organized and its supporting files close at hand.
Start with the document tree
Open the Document view from Interface > Document view, or use Ctrl+1 on Windows and Linux and Cmd+1 on Mac. The view displays the active document’s data graph: its nodes and their hierarchical relationships.
Rather than treating the tree as a passive inventory, use it to inspect and manage the contents of your workspace. You can select nodes, show or hide them, filter by node names or with Node Specification Language, and reorganize the hierarchy by dragging and dropping nodes. Context menus and the context toolbar provide actions for selected nodes.
Use folders to make groups manageable
When a document contains several related sets of nodes, folders give you a way to group them. For example, you might separate parts of a project that you want to inspect or show and hide together. Select Edit > Folder to create a folder; the shortcut is Ctrl+Shift+F on Windows and Linux or Cmd+Shift+F on Mac. Grouping related nodes can make common actions easier to apply and the document tree easier to scan.
Folders can also contain files. SAMSON stores embedded folders and files within the document, so the document can include supporting material such as PDFs, images, data files, structure files, and scripts. This is useful when you need to transfer a project or share it without leaving its supporting materials scattered across separate locations.
Keep alternatives separate, but easy to switch between
You can have several documents open at the same time, but only one is active in the Document view. This is useful when comparing or working on different molecules, or when you want to copy structures between documents without mixing their contents. Switch documents from the Documents list near the top-left of the menu or through Home > Documents. On Windows and Linux, use Ctrl+Tab and Ctrl+Shift+Tab to move between documents; on Mac, use Cmd+Tab and Cmd+Shift+Tab.
For a new task, create a clean document with Home > File > New, or use Ctrl+N on Windows and Linux and Cmd+N on Mac. To return to recently opened work, choose Home > File > Recent. Keeping distinct tasks in separate documents can reduce confusion while still letting you move between them when needed.
A small organization habit that helps at handoff
Before sharing or revisiting a project, take a moment to check the Document view: confirm that related nodes are grouped logically, add relevant supporting files to the document, and make sure you are working in the intended active document. These steps do not replace clear scientific notes, but they help keep the molecular model and useful project materials together.
For details on document contents, folders, files, and the Document view, see the SAMSON documents documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.