A molecular view can become hard to read for a simple reason: labels compete with the structure they are meant to explain. Atom names may be useful close up, while at a wider view they can overlap or turn into visual noise. The answer is not necessarily to remove labels altogether. In SAMSON, you can control which labels are visible at different zoom levels, then adjust their appearance and placement to support the task at hand.
A useful way to think about labels is as a changing layer of context. A label can show a node’s name, describe a group of nodes, or display a measurement. The right amount of detail depends on what you are examining and how closely you are viewing it.
Start with the nodes you need to explain
For a small number of labels, select the relevant structural nodes and use the label command in the context toolbar. Add label creates one label for the directly selected group. If you need labels on particular descendants—for example, residues within a selected structure—use Add label to… and choose the desired node type.
You can also add labels directly in the Viewport with the Label editor. The selection filter determines which type of node receives a label: for example, Atoms and bonds or Residues. Check that filter before placing labels; it is an easy setting to overlook when the result is not what you intended.
Let zoom determine the level of detail
Labels can change visibility progressively as you zoom. Smaller nodes, such as atoms, can disappear from view as you zoom out, while labels for larger nodes, such as molecules, can become visible. This helps avoid showing every level of detail at once.
If a label appears too early, stays visible too long, or is missing at a useful scale, select it and adjust its maximum and minimum display radii in the Inspector. These values govern when the label is visible. Rather than trying to show every label at every scale, use these settings to make the view reveal the level of detail that suits the current zoom.
You can also switch individual labels on or off in the Document view. This is a practical way to temporarily reduce clutter without deleting labels you may want to use later.
Make the text fit the purpose
For a consistent appearance across labels, change the default font in Preferences > Rendering > Labels. The same preferences include the number of decimal places used for angles and distances in measurement labels. For a specific label—or a selected group—use Choose font… in the Inspector. If you want selected labels to return to the default font, double-click the Font property in the Inspector.
Color can help distinguish labels, but it is also easy to create unnecessary visual emphasis. Set a constant color from the context toolbar, Visualization controls, or Inspector when it helps separate information. You can reset a label to its default color, and adjust its transparency in the Inspector.
Move labels when the structure needs room
Labels are initially placed at the geometric center of their nodes and remain in the plane of the Viewport. If a label obscures an important feature, select it and change its viewport offset in the Inspector, or move it with a Move editor. To move labels directly in the Viewport, set the selection filter to Labels first. Only visible labels can be selected there, so a hidden label may need to be made visible before you can reposition it.
A simple cleanup pass can make a view easier to interpret: keep only the labels relevant to the question, tune their display radii for different zoom levels, and move any that cover the structure. Labels are saved when the document is saved in SAMSON’s .sam or .samx formats, so this work can remain part of the document.
For the full instructions, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.