A molecular view can be scientifically accurate and still be hard to read. Atom labels may crowd a close-up, residue names can obscure a larger structure, and an important measurement can get lost among everything else. The answer is not always to remove useful context. In SAMSON, you can control which labels are visible at different zoom levels, then adjust their appearance and position to keep the view legible.
Think of labels as part of the visual hierarchy of a model: show the detail that matters at the current scale, and let less relevant detail recede.
Start with the right level of detail
Before adding labels, decide what you want the viewer to notice. A label can show a node’s name, describe a group of nodes, or display a measurement. Labels can be added to selected nodes from the context toolbar. Add label creates one label for the directly selected group; Add label to… lets you choose node types, including descendants such as residues within a selection.
Labels are mainly supported for structural nodes—such as molecules, residues, and atoms—not every node type. If you are adding labels in the Viewport, the active selection filter determines which type of node receives the label. Check the filter before placing a batch of labels; otherwise, you may be labeling a different structural level than intended.
Let zoom level guide visibility
Showing every label at every scale can make a molecular view feel crowded. SAMSON changes label visibility progressively as you zoom: labels for smaller nodes, such as atoms, begin to disappear when you zoom out, while labels for larger nodes, such as molecules, begin to appear. Zooming in reverses that pattern.
You can fine-tune this behavior for a particular label. Select it and use the Inspector to change its minimum and maximum display radii. These settings govern when that label is visible. This is useful when a specific name or annotation should remain available over a chosen range of views, rather than following the default visibility behavior.
Make an important label easier to read
If a label needs more emphasis, adjust its font or color. Preferences > Rendering > Labels changes the default font for labels that do not have a font specified directly. The same preferences also control the number of decimal places shown for angles and distances in measurement labels. For an individual label or selected group, use Choose font… in the Inspector. To return a label to the default font, select it and double-click Font in the Inspector.
Color can also distinguish an annotation from surrounding labels. Select a label and set Color > Constant from the context toolbar, Visualization controls, or Inspector. You can reset the color from the same controls, or clear the Inspector’s text color. Label transparency is adjustable in the Inspector as well.
Move labels without losing track of what they describe
New labels are placed at the geometric center of their nodes and lie in the Viewport plane. If one overlaps another label or a structural feature, you can select it and change its viewport offset in the Inspector. Alternatively, set the selection filter to Labels and use a Move editor, such as the Displace editor. You can also select a label in the Document view and move it with a Move editor.
To select labels directly in the Viewport, first set the selection filter to Labels. Only visible labels can be selected this way. Remember to switch the filter back before selecting other node types.
A quick labeling check
- Choose the structural level that answers the question your view is meant to address.
- Confirm the selection filter before adding labels in the Viewport.
- Zoom out and in to check whether labels remain readable at the scales you need.
- Adjust display radii, font, color, or offset only where they improve clarity.
- Save in a SAMSON format (.sam or .samx) if you want the labels saved with the document.
These small adjustments can make a model easier to inspect and easier to present without hiding the structural context. For the full instructions, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.