A molecular model can be scientifically clear and still be difficult to explain. Labels pile up over one another, small details compete with the overall structure, and a view that looked useful while zoomed in becomes confusing when zoomed out. The answer is rarely to label everything. A more reliable approach is to treat labels as a visual hierarchy: show the information that matters at the current scale, then make individual labels easy to distinguish and position.
In SAMSON, a label is a document node that displays text in the Viewport. It can show information such as a node’s name, a description of a group, or a measurement. Labels are saved with documents in SAMSON’s .sam and .samx formats, so the annotations can remain part of the saved model.
Start with the question, not the label tool
Before adding labels, decide what a viewer should notice first. For example, you might want to identify a molecule, point out selected residues, or make a measurement legible. These are different jobs, and they usually work better at different levels of detail. A label for a selected group can give context without naming every descendant; residue labels can then be added where residue-level detail is useful.
To label selected nodes, use the label command in the context toolbar. Add label creates one label for the currently selected group; it does not automatically label that group’s descendants. Use Add label to… when you want to choose a node type and include matching descendants, such as residues within the selection. Labels are mainly available for structural nodes, so they cannot be added to every type of node.
If you prefer to place labels directly in the Viewport, activate the Label editor in the Viewport’s left-side menu. The current selection filter determines what kind of node receives a label. For example, a filter set to Atoms and bonds targets atoms or bonds, while a filter set to Residues targets residues. Checking the filter before placing labels helps avoid annotating the wrong level of the structure.
Use zoom behavior to manage detail
One useful way to reduce clutter is to let label visibility change with scale. In SAMSON, labels for smaller nodes, such as atoms, progressively disappear as you zoom out, while labels for larger nodes, such as molecules, can appear. The reverse happens as you zoom in. This means the same scene can communicate broad structure at a distance and finer detail close up, without requiring every label to remain visible at once.
You can adjust when a particular label appears by selecting it and changing its maximum and minimum display radii in the Inspector. These settings govern the label’s visibility. If a scene becomes busy at a particular zoom level, review the display radii of the labels competing at that scale.
Make important labels distinct
When labels are visible together, consistent formatting makes them easier to scan. You can set the default font for labels in Preferences > Rendering > Labels. The same preferences also control the number of decimal places for angles and distances shown in labels, which can help keep measurements appropriately precise for the intended view.
For a particular label or group, select the labels and use Choose font… in the Inspector. You can edit the last selected label or choose to edit all selected nodes. If a label’s font should follow the general preference again, select it and double-click Font in the Inspector to reset it.
Color can also distinguish labels. Set a constant color through the context toolbar, the Visualization color controls, or the Inspector. If you later want the default color back, use Reset color or clear the text color in the Inspector. Transparency is adjustable in the Inspector as well. A practical rule is to use these options to clarify a label’s role, rather than making every annotation visually dominant.
Move labels only when placement gets in the way
New labels are placed at the geometric center of their nodes and remain in the Viewport plane. If text overlaps important structure or another label, select the label and adjust its viewport offset in the Inspector. You can also set the Selection filter to Labels and move labels with a Move editor, such as the Displace editor (shortcut D), or select a label in the Document view and use a Move editor there.
When selecting labels directly in the Viewport, set the Selection filter to Labels first. Only visible labels can be selected this way. Remember to switch the filter back afterward if you want to select other node types.
A useful finishing check is to inspect the scene at more than one zoom level: confirm that the broad view is not crowded, then zoom in to check that detailed labels remain readable. For more about creating, styling, selecting, and positioning labels, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.