A molecular view can be scientifically useful and still be difficult to read. Add labels to every atom or residue, and the structure may quickly become a wall of text. Hide too many, and the feature you meant to explain disappears. The goal is not to label everything at once: it is to make the right information visible at the right scale.
In SAMSON, labels are document nodes that display text in the Viewport. They can show node names, descriptions, or measurements, and are saved when you save a document in the .sam or .samx format. A little planning around what to label, when labels appear, and where they sit can make a model easier to inspect and present.
Start with the question your view should answer
Before adding labels, decide what a viewer needs to notice. If the point is to identify a molecule, a label for the selected group may be enough. If you need to compare particular residues, label those residues rather than every atom in the structure. For a measurement-focused view, use labels associated with the relevant measurement.
Select the intended nodes and use Add label in the context toolbar to create one label for the selected group. If you need labels on a particular node type within a selection, choose Add label to… and specify the type, such as residues. This distinction matters: the first command labels the directly selected group; it does not automatically label its descendants. Adding labels at a more useful structural level can preserve context without flooding the view with detail.
Let zoom level do some of the decluttering
Labels can change visibility as you zoom. By default, labels for smaller nodes, such as atoms, start to disappear as you zoom out, while labels for larger nodes, such as molecules, start to appear. Zooming in reverses that pattern. This helps keep fine-grained annotations from dominating a distant view while making them available when you inspect the structure more closely.
If a label appears too early, disappears too soon, or is visible at an unhelpful scale, select it and adjust its maximum and minimum display radii in the Inspector. These settings control when the label is displayed. It is often useful to review the view at both close and distant zoom levels after changing them: a label that reads well up close may overlap other text when the whole system is in view.
Make important labels easy to find
When labels overlap the structure or one another, moving them can improve readability without changing the molecular model. A newly created label is placed at the geometric center of its node and lies in the Viewport plane. To reposition one, select it and change its viewport offset in the Inspector, or use a Move editor. For moving labels directly in the Viewport, set the Selection filter to Labels first. The Displace editor is one option; its shortcut is D.
Selection filters are worth checking before both selection and movement. If the filter is set to another node type, clicks in the Viewport will not target labels as intended. When you are finished arranging them, switch the filter back if you want to select other kinds of nodes. You can also select a label in the Document view and use a Move editor.
Use a consistent visual treatment
Font and color can help distinguish annotations, but consistency usually makes a model easier to scan than giving every label a different style. Set the default font for labels in Preferences > Rendering > Labels. For a specific label or group, select the labels and choose a font in the Inspector. You can also reset a label’s font to the preference default by double-clicking Font in the Inspector.
To change a label’s color, use Color > Constant from the context toolbar, Visualization controls, or Inspector. The Inspector also lets you adjust label transparency. If a custom color is no longer useful, reset it using the color controls or clear the text color in the Inspector. For measurement labels, the label preferences also include the number of decimal places shown for angles and distances.
A quick readability check
Before sharing a scene, try this short review: confirm that each label answers a specific question; check that labels are attached to the intended node level; zoom in and out to see whether display radii behave as expected; move labels that obscure important features; and verify the selection filter before editing labels in the Viewport. Saving as .sam or .samx preserves the labels with the document.
For the full labeling guide, including adding, selecting, styling, and moving labels, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.