A molecular view can become hard to interpret for two opposite reasons: important features are not labeled, or so many labels compete for attention that the structure is difficult to see. The challenge is especially noticeable when you zoom between an overview of a system and a close-up of its atoms or residues.
In SAMSON, labels are document nodes that display text in the Viewport. They can show node names, describe groups, or display measurements. A practical way to keep annotations useful is to decide what level of the structure deserves a label at each viewing scale, then adjust visibility and placement to support that purpose.
Start with the right level of detail
Before adding labels, consider what you want the current view to communicate. For a broad overview, labels on larger structural nodes—such as molecules—may be more useful than labels on every atom. For a close-up analysis, residue- or atom-level labels may be appropriate.
Select the relevant nodes and use the context toolbar’s label command. Add label creates one label for the directly selected group; it does not automatically label that group’s descendants. Use Add label to… when you want to choose a node type, including descendants—for example, to label residues within a selected region.
You can also add labels directly in the Viewport with the Label editor. The node type affected depends on the current selection filter: a filter set to Atoms and bonds targets atoms or bonds, while Residues targets residues. Checking the filter before labeling helps avoid creating annotations at the wrong structural level.
Let zoom guide what appears
Label visibility changes progressively as you zoom. 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 behavior can help preserve context across scales without requiring every label to remain visible at once.
If a label appears too early, disappears too soon, or otherwise does not suit your view, select it and adjust its maximum and minimum display radii in the Inspector. These settings govern when the label is visible. It is useful to review them at both a close-up and an overview scale, rather than judging the result at only one zoom level.
You can also hide or show individual labels by ticking or unticking them in the Document view. This provides a quick way to reduce clutter temporarily while keeping the labels in the document.
Make annotations readable
When labels overlap important visual details, move them rather than changing the structure. Labels are initially placed at the geometric center of their nodes and lie in the Viewport plane. You can select a label and adjust its viewport offset in the Inspector, or set the selection filter to Labels and use a Move editor, such as the Displace editor. You can also select a label in the Document view and use a Move editor.
For a group of labels that needs a consistent appearance, select them and use Choose font… in the Inspector. To change the font used by labels without an individually specified font, use Preferences > Rendering > Labels. That preference also controls the number of decimal places shown for angles and distances in measurement labels.
Labels can be colorized and their transparency adjusted in the Inspector. A restrained color choice can help distinguish an annotation from the structure, while keeping the text readable against the current view. If a label’s color or font no longer fits, reset it to the default rather than leaving an accidental override in place.
A simple final check
Before sharing a view, check it at the zoom levels your audience is likely to use. Confirm that the intended labels are visible, that the selection filter is set appropriately before selecting or moving labels in the Viewport, and that annotations do not obscure the feature being discussed. If you plan to preserve the work, save the document in SAMSON’s .sam or .samx format; labels are saved with those documents.
For details on label creation, visibility, styling, selection, and positioning, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.