Selecting the right atoms or molecular components can be surprisingly difficult. A click in the 3D view may pick an unexpected node, while a large document hierarchy can make it hard to locate a specific part of a structure. The key is to choose the selection method that fits the task: use the viewport for visual picking, the Document view for navigating the hierarchy, and a search expression when you need to find nodes by specification.
1. Start with the viewport when the target is visible
Activate a selection editor, then select nodes directly in the viewport. If the structure is crowded, first check the selection filter at the top-right of the viewport. It controls which node types can be highlighted and selected. For example, if you are trying to work with atoms but a click keeps targeting a larger structural component, review the filter before repeatedly clicking.
The Rectangle selection editor is a useful default for this workflow. Press R to activate it. Click a node to select it, or drag outside selected nodes to make a rectangular selection. Hold Ctrl on Windows/Linux or Cmd on macOS to add nodes to the selection; hold Alt to remove nodes. Right-click to open the context menu.
2. Switch to the Document view when the hierarchy is clearer
Sometimes the structure is easier to understand as a tree than as a 3D scene. In the Document view, click nodes to select them and highlight them in the viewport. Use Shift and Ctrl or Cmd to make a multi-selection. This is especially helpful when you know the name or location of a node but cannot easily distinguish it visually.
You can filter the Document view by entering text or a Node Specification Language (NSL) expression. Press Enter to select the matching nodes. The selection filter in this view is separate from the viewport filter, so check that the filtering method you are using matches the place where you are searching.
3. Use Find for criteria-based selection
When selecting by a specification is more reliable than locating nodes by eye, use Select > Find. The shortcut is Ctrl+F on Windows/Linux or Cmd+F on macOS. Find uses the Node Specification Language, which can help select nodes based on criteria rather than their screen position. If you are new to NSL, start with a simple expression and consult the Node Specification Language guide for the syntax.
After making a selection, look at the bottom of the Document view for the selection summary. Clicking the summary opens contextual actions for the current selection. It is a useful checkpoint: before moving or modifying anything, confirm that the selection represents the nodes you intended to work with.
4. Inspect before making changes
If you are unsure what a selected node represents, open the Inspector from Interface > Inspector, or use Ctrl+2 / Cmd+2. The Inspector displays properties of selected nodes and lets you filter attributes. This creates a simple, dependable loop: select, check the selection summary, inspect relevant properties, then proceed with the intended action.
For instance, once you have confirmed a selection, you can choose a visual model to change how it is displayed, or use the selection as the scope for a simulation. SAMSON’s quick-start guide explains these workflows and links to more detailed pages on selecting, inspecting, and modeling and simulation.
A small habit that prevents big mistakes
Before an action that changes a structure or starts a simulation, pause to verify the selection. Use the viewport when visual location matters, the Document view when hierarchy matters, and Find when a specification matters. Check the selection summary, then inspect the nodes if their identity or properties are uncertain. This takes only a moment and helps avoid applying an operation to the wrong part of a molecular model.
For more interface basics and links to related workflows, see the SAMSON Quick Start Guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.