A common molecular-modeling frustration is selecting what looks like one thing in the viewport, then discovering that the selection contains much more—or less—than intended. A residue, its backbone, and its side chain are related nodes in the document, and a name-based filter may match several of them. The result can affect whatever you do next: inspection, editing, visualization, or simulation setup.
A reliable approach is to be deliberate about what level you are selecting and how precisely you describe it. In SAMSON, you can combine the viewport selection filter with the Node Specification Language (NSL), then save useful selections for quick reuse.
First, choose the right selection level
The selection filter is in the top-right corner of the viewport. It controls the node level used by the rectangle selection editor and some other editors. For example, with the filter set to Residues, clicking an atom selects its residue rather than just that atom. With Atoms, the selection operates at the atom level. The default is Any node.
This distinction matters when you are selecting visually. Before clicking or dragging a selection rectangle, check the filter: it can explain why a click on one atom selected an entire residue. The same filter also affects Select all, which selects all selectable nodes at the chosen level.
Use an exact expression when names are ambiguous
Filtering by a plain string in the Document view is convenient, but it searches node names. That can be broader than expected. For example, typing LYS may select lysine residues along with their backbones and side chains because those node names also contain “LYS.” In the documented example, that produces 15 selected nodes even though the structure contains only 5 LYS residues.
To target the residues themselves, use an NSL expression in the Document view’s Filter nodes… box, then press Enter to select the matching nodes:
residue.type LYS
The shorter form, r.t LYS, expresses the same selection. The practical lesson is simple: if a name search gives you unexpected results, switch from matching text to specifying a node property. You can also use the Find window to enter NSL expressions. This makes it easier to describe the selection you mean instead of relying on similar names.
Turn a useful selection into a repeatable tool
If you often need the same kind of selection, save the expression as a custom selection filter. Open Select > Find, or use Ctrl/Cmd + F, enter the expression, click Save, and give the filter a recognizable name. For example, r.t LYS or r.t HIS can be saved as “LYS and HIS residues.” The saved filter then appears in the selection-filter list.
This reduces repetitive typing and makes a useful selection rule easier to apply again. Custom filters can be removed by making one active and right-clicking the selection-filter list. Choosing Reset selection filters removes all filters you added, so use that option only when you intend to clear them all.
Keep working selections close at hand
For selections you want to revisit while working in a document, Quick Groups provide a fast switching workflow. Select a region, then assign it to a slot by hovering over the slot in the Document view and pressing Shift + click, or by pressing Shift plus a number. You can create up to 10 Quick Groups. Press the corresponding number key to switch to that selection; double-press the number to zoom to it.
For example, you might assign a ligand, receptor, and water molecules to three separate groups, then switch between them while inspecting the structure. Quick Groups are temporary and can be redefined, which makes them handy for selections you need during the current workflow. For named groups that you want to see in the document, right-click a selection and choose Select > Group.
When selecting through the Document view, Ctrl/Cmd + click adds or removes individual nodes, while Shift + click selects consecutive nodes. In the viewport, the rectangle selection editor uses Ctrl to add and Alt to remove nodes. These modifiers help refine a selection without starting over.
A useful sequence is: set the selection level, express the target precisely with NSL when names are ambiguous, check the selection summary, and save or assign the result if you will need it again. To explore the available commands, filters, and selection methods, see the SAMSON selection documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.