A molecular view can be scientifically informative and still be difficult to read. Labels overlap, small details compete with larger structural features, and a view that looks clear when zoomed in may become cluttered when zoomed out. The goal is not simply to add more text—it is to make the right information visible at the right moment.
In SAMSON, labels are document nodes that display text in the Viewport. They can identify structural nodes or show descriptions and measurements, and they are saved when you save the document in .sam or .samx format. A useful approach is to add labels deliberately, then tune their visibility and placement for the view you need.
Start with the audience and the scale
Before adding labels, decide what the viewer should notice. If the point is to identify a selected group, use Add label from the selection’s context toolbar. This creates one label for the directly selected group. If you need names for individual structural parts—such as residues within a selected region—use Add label to… and choose the node type. This can include descendants of the selected nodes.
That distinction helps avoid a common source of clutter: creating a label for every small component when one group label would communicate the same point. The context toolbar provides both options:
You can also add labels directly in the Viewport with the Label editor. The type of node labeled depends on the current selection filter. For example, an “Atoms and bonds” filter targets atoms or bonds, while a “Residues” filter targets residues. Check the filter before labeling so the result matches your intention.
Let zoom level help manage clutter
Labels change visibility progressively as you zoom. Labels associated with smaller nodes, such as atoms, can disappear as you zoom out, while labels for larger nodes, such as molecules, can become visible. This behavior helps keep the view useful across scales, but the display range can be adjusted when a particular label appears too early or too late.
Select the label and, in the Inspector, adjust its maximum and minimum display radii. These settings govern when the label is visible. It is worth checking the result at both close and distant zoom levels: a setting that improves one view may not suit another.
For a quick overview of which labels are enabled, use the Document view to switch their visibility on or off. This can be useful when preparing different views of the same structure without removing labels from the document.
Improve legibility without changing the science
When several labels need to be read together, consistent typography can make the annotation easier to scan. To change the default font for labels that do not have an individually specified font, use Preferences > Rendering > Labels. The same preferences let you set the number of decimal places for angles and distances shown in measurement labels.
For a particular label or selected group, choose a font in the Inspector. You can edit the last selected label, or choose Edit all selected nodes to apply the change to all selected nodes. Double-clicking the Font property resets selected labels to the font specified in Preferences.
Color can also distinguish annotations. A label’s color can be changed through the context toolbar, the Visualization color controls, or the Inspector. The Inspector also lets you adjust transparency. If a custom color is no longer useful, reset it using the color controls or the clear button next to Text color in the Inspector.
Move labels away from crowded regions
Labels are initially placed at the geometric center of their nodes and lie in the Viewport plane. If text obscures a 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), or select a label in the Document view and move it with a Move editor.
A practical finishing pass is simple: show only the labels relevant to the current explanation, inspect them at the zoom levels you expect to use, adjust their display radii, and move any that cover important details. When selecting or moving labels in the Viewport, set the selection filter to “Labels”; switch it back afterward if you want to work with other node types. Only visible labels can be selected there.
For the full labeling workflow, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.