When you are working with a molecular model, the structure itself is only part of the task. You may also need to find a residue, inspect an atom, change a visual representation, compare documents, or undo a recent operation. If you are not sure where those controls live, small interface detours can interrupt the scientific work.
A useful way to navigate SAMSON is to think in terms of the job you are doing: locate and organize structures, inspect their properties, choose an editing tool, then review or present the result. The interface is arranged to support these different kinds of work, and knowing which area to reach for can make common tasks easier to follow.
Start with the document structure
The Document view is the place to understand what is inside the active document. It displays the document’s hierarchical data graph, so you can browse its organization rather than relying only on what is visible in the viewport. From here, you can select or hide nodes, filter them by name or with Node Specification Language, and reorganize the structure by dragging and dropping nodes.
This is especially useful when a scene contains many components or when an object is difficult to pick directly in the viewport. Select a node in the Document view, then use the Inspector to examine or edit its properties.
Use the Inspector for properties
The Inspector displays properties for selected nodes. One detail matters when working with multiple selections: it inspects all selected nodes and applies edits to all of them. Before changing a value, check which nodes are selected. If the list is larger than intended, narrow the selection first.
The Inspector’s filter can help you find matching attributes without scanning every property. This makes it a practical next step after locating a node in the Document view: choose the relevant node or nodes, open the Inspector, and filter the properties you need to review.
Choose tools by the kind of action
For commands that change the document, the ribbon menus provide organized options. The Home menu includes document tasks such as opening, saving, and fetching structures, along with structure-related actions such as preparation, validation, and visualization. Edit groups together undo and redo, clipboard actions, adding document items, hydrogen adjustments, object organization, and simulation controls. Select contains search and selection operations.
When you are focused on the viewport, the editor menu offers another route to tools. It includes commonly used editors such as View, Point selection, Rectangle selection, Add, Bonds, and move editors. The listed keyboard shortcuts can make frequent actions easier to reach: for example, V selects View, P selects Point selection, and A selects Add. The Find everything box is useful when you know the name of a command, app, or editor but not which menu contains it; it searches names, tooltips, and shortcuts.
Keep track of documents and changes
SAMSON can have several documents open, but only one is active at a time. Switching documents is useful when working with different molecules or copying structures between documents. You can switch from the Documents list or through Home > Documents. The shortcuts are Ctrl/Cmd + Tab and Ctrl/Cmd + Shift + Tab.
If you need to revisit an earlier undoable state, open History. Selecting an entry returns the document to its associated state. However, not every operation is undoable, and the documentation cautions that non-undoable operations between undoable ones can affect whether SAMSON can properly undo changes. Treat History as a helpful record, not a substitute for saving important work.
A practical navigation loop
- Locate: browse or filter the Document view to find the structure or node.
- Select: check the selection before applying an action, especially if multiple nodes may be selected.
- Inspect: use the Inspector and its filter to review relevant properties.
- Act: choose a command from the ribbon, the viewport editor menu, or Find everything.
- Review: use History when you need to return to an undoable state, and save important document changes.
This small sequence gives each part of the interface a clear role: the Document view helps you locate and organize, the Inspector helps you examine, the menus and editors help you act, and History helps you review changes. For shortcuts, panel details, and the full menu reference, see the SAMSON Interface documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.