A molecular view can be easy to understand at one scale and confusing at another. Zoom in, and atom labels may crowd the structure; zoom out, and the detail you were using to orient yourself can disappear. That makes labels more than decoration: they need to support the question you are asking at the current view.
In SAMSON, labels are document nodes shown in the Viewport. They can identify structural nodes, describe a group, or display a measurement. The key to keeping a view clear is to treat labels as a layer of information: add the ones you need, control when they appear, and move or style them when they compete with the structure.
Start with the right labeling level
Before adding labels, decide whether you need to identify a selected group or its parts. The context toolbar’s Add label command creates one label for the directly selected group; it does not label that group’s descendants. Use Add label to… when you want labels on a chosen node type among the selection’s descendants—for example, residues.
This distinction helps avoid a common source of clutter: labeling many small components when a single group label would answer the question. Conversely, if your task depends on identifying individual residues, labeling only the whole selection will not provide that detail. Labels are available mainly for structural nodes, so they cannot be applied to every node type.
Let zoom determine what stays visible
Labels can change visibility progressively as you zoom. Smaller-node labels, such as atom labels, start to disappear as you zoom out, while labels for larger nodes, such as molecules, can appear. Zooming in reverses that pattern. This lets the view present different levels of annotation at different scales instead of asking every label to remain legible all the time.
If a particular label appears too early, too late, or not at the scale you need, select it and adjust its maximum and minimum display radii in the Inspector. These settings govern when it is visible. You can also use the Document view to switch individual labels on or off while keeping them in the document.
Make important labels easy to read
When labels overlap or sit on top of an important feature, reposition them rather than changing the molecular structure. A label begins at the geometric center of its node and remains in the Viewport plane. You can select it and edit its viewport offset in the Inspector, or use a Move editor. To move labels directly in the Viewport, set the selection filter to Labels first. Remember to switch the filter back when you want to select other node types.
For a consistent presentation, font and color can be adjusted at different levels. Preferences > Rendering > Labels sets the font for labels without a font specified directly. To change one or more specific labels, select them and use Choose font… in the Inspector; you can also reset their font to the preference. A constant color can be set through the context toolbar, Visualization controls, or Inspector, and reset in the same places. The Inspector also lets you adjust label transparency.
A practical sequence is to label the structural level relevant to your question, check the result at both close and overview zooms, adjust display radii where needed, then move or style only the labels that remain difficult to read. If you save the document as a SAMSON file (.sam or .samx), its labels are saved with it.
For the full instructions, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.