SAMSON documents are hierarchies of SAMSON nodes (see node types for the description of types of nodes in SAMSON documents). A document hierarchy is visible in the document view.

SAMSON documents may contain cameras, folders, structural nodes (e.g. molecules, residues, atoms, groups), conformations, paths, and notes. The loaded or created molecules are placed in the active document. SAMSON documents store all information about atoms, bonds, molecules, models, simulators, etc.

The document view can be opened via Interface menu > Document view or via the Ctrl + 1 shortcut on Windows and Linux or Cmd⌘ + 1 on Mac.

The document view shows SAMSON document structure

The document view shows the data graph (hierarchical structure) of an active document. You can filter the nodes using Node Specification Language and names of the nodes. See node types for more details on types of nodes in the SAMSON document.

In one SAMSON instance you may simultaneously have multiple opened documents, but only one document is active at any given time - the one you see in the document view. Having several documents is useful when you want to do different not-connected tasks with different molecules.

To create a new document, click on New... in the Home menu or use the Ctrl + N shortcut on Windows and Linux or Cmd⌘ + N on Mac.

To switch between documents, use the Home menu, or the Ctrl/ Cmd⌘ + Tab or Ctrl/ Cmd⌘ + Shift + Tab shortcuts.

Switching between documents

To open recently opened documents, use Recent in the Home menu.


A Document may have several folders which can be used to arrange any types of nodes together, to apply operations to sets of molecules, e.g. hide or show them in one click. To create a new folder, use the Ctrl + Shift + F shortcut on Windows and Linux or Cmd⌘ + Shift + F on Mac or click on Add folder... in the Edit menu.

Edit menu