A molecular view can be scientifically rich and still be difficult to read. Atom names, residue identifiers, group descriptions, and measurement values all compete for space—especially when you zoom out or need to show someone else a specific feature. Labels help only when the right information is visible at the right moment.
In SAMSON, labels are document nodes that display text in the Viewport. They can describe a structural node or group, or show a measurement. The useful part is that you can control not just what labels say, but also which labels appear, how they look, and where they sit.
Start with the right labeling scope
Before adding labels, decide whether you need one annotation for a selected group or individual labels for structural components within it. From the selection’s context toolbar, Add label creates a single label for the directly selected group. It does not label that group’s descendants. Use Add label to… when you want to choose a node type among the selection’s descendants—for example, residues.
You can also add labels directly in the Viewport with the Label editor. In that workflow, the current selection filter determines what kind of node receives the label. A filter set to “Atoms and bonds” targets atoms or bonds; a filter set to “Residues” targets residues. Checking this setting first can prevent the common mismatch between the feature you intended to annotate and the node that actually gets labeled.
Use zoom behavior instead of showing everything at once
Labels do not all need to remain visible at every viewing scale. SAMSON progressively changes label visibility as you zoom: labels for smaller nodes, such as atoms, start disappearing as you zoom out, while labels for larger nodes, such as molecules, start appearing. The reverse happens as you zoom in.
If a particular label appears too early, too late, or at an inconvenient scale, select it and adjust its minimum and maximum display radii in the Inspector. These settings govern when that label is visible. This lets you tune labels to the scale at which their text is useful, rather than treating visibility as simply on or off.
For a quick manual cleanup, labels can also be shown or hidden by ticking or unticking them in the Document view. That is useful when you want to temporarily reduce visual noise without changing the label’s text or other properties.
Make annotations legible, not louder
For labels that need a different typeface, select one or more labels and use Choose font… in the Inspector. You can edit the last selected label or, by choosing Edit all selected nodes, apply the change to the selected labels together. To return a label to the font set in Preferences, double-click its Font property in the Inspector. Preferences also control the default label font and the number of decimal places used for angles and distances in measurement labels.
Color can help distinguish labels, but it is also possible to reset a label to its default color if a custom choice is no longer useful. You can change or reset color through the context toolbar, Visualization controls, or the Inspector. The Inspector also provides a transparency setting.
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. When text overlaps another feature, select the label and adjust its viewport offset in the Inspector. Alternatively, set the selection filter to “Labels” and use a Move editor, such as the Displace editor (shortcut: D). You can also select a label in the Document view and move it with a Move editor.
If you select labels in the Viewport, first set the selection filter to “Labels.” Only visible labels will be selected, and you will need to change the filter back when you want to select other node types. This small check helps avoid accidentally manipulating the molecular structure when your goal is to tidy annotations.
Finally, labels are saved with the document when you use a SAMSON format such as .sam or .samx, so your annotations can remain part of the saved model. For more details, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.