A molecular model can be scientifically useful and still be difficult to read. Atom names, residue labels, and measurements may all be relevant, but when they appear together in a crowded view, it can be hard to see the feature you are trying to explain. The solution is not always to remove information. Often, it is to control which labels appear, when they appear, and where they sit.
In SAMSON, labels are document nodes that display text in the Viewport. They can show a node’s name, describe a group, or present a measurement. Because labels are part of the document, they can also be saved with it in the .sam or .samx formats.
Start with the question your view should answer
Before adding labels, decide what someone should notice first. Are you identifying a particular residue, comparing parts of a structure, or presenting a measurement? This small pause helps avoid labeling every possible node simply because the option is available.
Select the relevant nodes and use the context toolbar. Add label creates one label for the directly selected group. Add label to… lets you choose a node type and can include descendants—for example, adding labels to residues within a selected group. Labels are mainly available for structural nodes such as molecules, residues, and atoms, rather than every node type.
For labels placed directly in the Viewport, activate the Label editor. The type of node that receives a label depends on the current selection filter: a filter set to Atoms and bonds targets atoms or bonds, while a Residues filter targets residues. Checking this filter first can prevent the common frustration of labeling the wrong level of the structure.
Let zoom determine the level of detail
A view that works close up may become cluttered when you zoom out. SAMSON handles this progressively: labels for smaller nodes, such as atoms, can disappear as you zoom out, while labels for larger nodes, such as molecules, can appear. The reverse happens as you zoom in. This makes it possible to use different levels of labeling without expecting every label to remain visible at every scale.
If a label appears at an unhelpful scale, select it and adjust its maximum and minimum display radii in the Inspector. These settings control when that label is visible. A practical way to tune them is to zoom through the range in which you expect to use the view and adjust the settings until the relevant labels appear at useful scales.
Separate visibility from selection
When labels are in the way, you do not necessarily need to delete them. In the Document view, tick or untick labels to show or hide them. This lets you keep useful annotations in the document while choosing which ones are visible for a particular view.
You can also select labels in the Viewport, but first set the selection filter to Labels. Only visible labels will be selected. When you are done, switch the filter back if you want to select atoms, residues, or another node type. Remembering this step avoids accidentally selecting a different part of the model while trying to edit an annotation.
Make room without losing the connection
Labels are initially placed at the geometric center of their nodes and lie in the Viewport plane. If text overlaps another feature, select the label and change its viewport offset in the Inspector, or use a Move editor with the selection filter set to Labels. You can also select a label in the Document view and move it with a Move editor. After moving labels, check the view again at the zoom levels where you plan to use it.
For a clean handoff, keep the annotations that answer the viewer’s question, use display radii to manage scale, hide labels that are not needed in the current view, and reposition only those that obscure important features. This preserves useful context without making every part of the structure compete for attention.
For the full instructions on adding, displaying, styling, and moving labels, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.