In a molecular model, selecting the right atoms can be harder than it looks. A click may pick the wrong kind of node, a crowded viewport can make small targets difficult to isolate, and a selection that was useful a moment ago can be difficult to recreate. A reliable workflow combines viewport selection, the Document view, and text-based filtering—so you can choose, check, and reuse the nodes you actually mean to work with.
Start by choosing what can be selected
In the viewport, activate a selection editor and use the mouse to select nodes. If the wrong kinds of objects keep getting highlighted, check the selection filter in the top-right corner of the viewport. It controls which node types can be highlighted and selected. Adjusting the filter first can make selection less confusing, especially when a document contains several kinds of nodes.
For mouse-based selection, the Rectangle selection editor is a useful starting point. Press R to activate it. Click nodes to select them, 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.
Use the Document view when the viewport is crowded
The Document view gives you another way to select nodes: click an entry in the hierarchy to select it and highlight it in the viewport. Use Shift and Ctrl or Cmd for multi-selection. Its filter can narrow the displayed nodes by text or by a Node Specification Language (NSL) expression. Press Enter to select the matching nodes.
This is particularly helpful when you know something about the target—such as its name or the type of node you need—but cannot easily pick it in the 3D view. The viewport is useful for spatially locating objects; the hierarchy and its filter are useful for finding nodes by document structure or matching criteria. You can switch between the two rather than relying on one method for every task.
Check the selection before acting
Before moving, editing, or applying a tool, pause to verify what is selected. The bottom of the Document view displays a summary of the current selection. Click the summary to open contextual actions for that selection. This small check can help catch an accidental extra node—or a selection that contains fewer nodes than intended—before you make a change.
When a matching rule is more useful than browsing the hierarchy, use Select > Find. The shortcut is Ctrl+F on Windows/Linux or Cmd+F on macOS. Find uses the Node Specification Language, letting you select nodes by an expression rather than by individual clicks. If you are new to NSL, begin with a simple criterion, inspect the selection summary, and refine the expression if the result is not what you expected.
Save selections you will need again
If a selection represents a useful set of nodes, save it as a node group instead of rebuilding it from scratch. Use Select > Group or press G to create a group from the current selection. Later, double-click the group in the Document view to restore that selection. This is a practical way to keep recurring targets accessible while working through a document.
A dependable selection routine is simple: set the viewport filter, select with the method that best suits the task, inspect the selection summary, and group selections worth keeping. For more details, see the SAMSON Quick Start Guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.