A molecular scene can be scientifically informative and still be hard to read. Atom names, residue annotations, and measurement labels may overlap, compete for attention, or disappear when you change the view. The goal is not to label everything at once: it is to make the right information visible at the right scale, then position and style it so it supports the structure.
Start with the level of detail you need
In SAMSON, labels are nodes stored in the document, and they can describe a selected group, identify structural nodes, or display measurements. Before adding them, decide what a viewer needs to identify. A group-level label can orient someone to a region; labels on residues can help compare local features. Adding labels only to the level you need is a practical way to avoid unnecessary visual noise.
Select the relevant nodes and use the context toolbar. Add label creates one label for the directly selected group. It does not automatically label descendant nodes. Use Add label to… when you want labels on a chosen type of node, including descendants—for example, residues within a selected group.
You can also add labels directly in the Viewport with the Label editor. In this case, the selection filter matters: it determines which type of node receives the label. Set the filter deliberately before labeling, such as Residues for residue labels or Atoms and bonds for those structural elements.
Use visibility to manage density
When many labels are present, visibility controls can be more useful than deleting annotations you may need later. In the Document view, tick or untick labels to show or hide them. You can also select a label and adjust its maximum and minimum display radii in the Inspector. These settings control the range at which it appears.
Labels can change visibility progressively as you zoom. Smaller-node labels, such as atom labels, can disappear as you zoom out, while labels for larger nodes, such as molecules, can become visible. This helps the scene present different levels of information at different viewing scales. If the transition does not suit your view, adjust the label’s display radii rather than assuming the label has been removed.
Move labels out of the way
New labels are placed at the geometric center of their nodes and lie in the Viewport plane. When a label obscures a feature or another annotation, you have several ways to reposition it. Select it and change its viewport offset in the Inspector, or set the selection filter to Labels and use a Move editor. You can also select the label in the Document view and move it with a Move editor.
Remember to restore the selection filter when you want to select other kinds of nodes in the Viewport. The filter determines what you can select there, so leaving it on Labels can make later selection behave differently than expected.
Make important labels easy to distinguish
For a consistent appearance, set the default font in Preferences > Rendering > Labels. You can also set the number of decimal places shown for angles and distances—useful for labels created with the Measure editor. To style an individual label or a group, select the labels and use Choose font… in the Inspector. To change the font of all selected labels together, choose Edit all selected nodes. Double-click the Font field to reset selected labels to the preference default.
Color can also distinguish annotations. Apply a constant color from the context toolbar, Visualization controls, or Inspector. If you want to return to the default, use Reset color or clear the Text color in the Inspector. The Inspector also lets you adjust label transparency.
A useful finishing pass is to check the scene at the zoom levels where it will be viewed: hide labels that are not needed, tune display radii, move collisions, and use font or color changes sparingly to clarify categories. If you save the document as a SAMSON .sam or .samx file, its labels are saved with it.
For more details, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.