Selecting the right part of a molecular model can be harder than it sounds. In a crowded structure, a click may pick the wrong node; a rectangle can include more than intended; and a selection that looks right in the viewport may be difficult to check. A reliable approach is to combine three views of the same task: select visually, refine in the Document view, and verify the result before acting on it.
This workflow is useful before editing, measuring, inspecting, or applying a visual model. The key idea is to treat selection as something you can inspect and refine—not just a click you hope was accurate.
1. Start with the viewport, but control what can be selected
Choose a selection editor from the left-side menu in the viewport. The default Rectangle selection editor is available with R. Click nodes to select them, or drag outside selected nodes to draw a rectangle. Hold Ctrl on Windows and Linux, or Cmd on macOS, to add nodes to the selection; hold Alt to remove nodes.
When the structure is visually dense, first check the selection filter in the top-right corner of the viewport. It controls which node types can be highlighted and selected. Narrowing the selectable types can help prevent an atom-level task from accidentally selecting a larger structural component.
2. Refine the selection in the Document view
The viewport is convenient for choosing a visible region. The Document view is useful when you need to work with the document hierarchy or select nodes by name or specification. Click a node there to select it and highlight it in the viewport. Use Shift and Ctrl or Cmd for multi-selection.
You can also enter text or a Node Specification Language (NSL) expression in the Document view filter, then press Enter to select matching nodes. This is especially useful when a target is hard to isolate by clicking in a busy 3D view. The Document view filter gives you another way to express what you mean, while the viewport shows where the resulting selection is located.
3. Check the selection before changing anything
Before applying an operation, pause and check the selection summary at the bottom of the Document view. Clicking the summary opens contextual actions for the current selection. This is a useful checkpoint: if the selection is not what you intended, refine it before you move, measure, or otherwise work with those nodes.
For a more direct query workflow, use Select > Find with Ctrl+F on Windows and Linux, or Cmd+F on macOS. The Find command selects nodes using NSL. Once selected, double-clicking an atom or bond in the Document view selects it and zooms to it, which can help you check an individual target in context.
4. Inspect properties when identity matters
If you need to confirm what a selected node is, open the Inspector with Interface > Inspector, Ctrl+2 or Cmd+2. It displays properties of selected nodes, and its filter can narrow the attributes shown. This gives you a way to check node details instead of relying only on its appearance in the viewport.
A small habit that prevents avoidable mistakes
Use a simple sequence: set the selection filter, select in the viewport or Document view, review the selection summary, and inspect properties if needed. For repeatable tasks, save the current selection as a node group with Select > Group or the G shortcut; double-click the group later to restore the selection.
This approach doesn’t replace careful modeling, but it makes selection easier to reason about: one interface helps you locate nodes, another helps you define them, and the summary and Inspector help you check what you’re about to work on.
For more on selection tools and the rest of the interface, see the SAMSON Quick Start Guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.