A molecular scene can be scientifically rich and still be difficult to read. Labels that overlap, disappear at the wrong zoom level, or identify the wrong level of structure can make it harder to explain what matters. A useful approach is to treat labels as part of the scene’s visual hierarchy: decide what needs to be named, control when labels appear, and move them only when their placement obscures the structure.
In SAMSON, a label is a document node that displays text in the Viewport. It can show a node’s name, describe a group of nodes, or display a measurement. Labels are mainly available for structural nodes such as molecules, residues, and atoms. If you save the document as a .sam or .samx file, its labels are saved too.
Start with the level of detail you need
Before adding labels, consider what a viewer should be able to identify. For a whole-molecule overview, a label for the selected group may be enough. For a closer view, labels on residues or atoms may be more useful. The context toolbar offers two distinct choices:
- Add label creates one label for the directly selected group. It does not automatically label that group’s descendants.
- Add label to… lets you choose node types to label, including descendants—for example, residues within the selected nodes.
This distinction helps avoid a common source of visual clutter: labeling every detail when the scene only needs to communicate the larger structure. If you are adding labels directly in the Viewport, activate the Label editor first. The current selection filter determines what kind of node receives a label, so check it before placing labels.
Use zoom behavior to manage density
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 lets a scene reveal detail at closer views without requiring every label to stay on screen at once.
If a label appears too early, too late, or at an unhelpful scale, select it and adjust its maximum and minimum display radii in the Inspector. These settings govern when that label is visible. You can also turn individual labels on or off in the Document view—handy when you want to simplify a scene without deleting labels you may need again.
Make room without losing the connection
New labels are placed at the geometric center of their nodes and lie in the Viewport plane. If a label overlaps important visual detail, select it and change its viewport offset in the Inspector. Alternatively, set the selection filter to Labels and use a Move editor, such as the Displace editor (shortcut: D), to reposition it in the Viewport. You can also select a label in the Document view and move it with a Move editor.
Moving labels is especially useful when several important annotations occupy the same area. Make small adjustments, then check the scene at the zoom level where it will be viewed. A position that works in a close-up may not be as clear when zoomed out.
Keep selection and appearance under control
To select labels in the Viewport, first set the Selection filter to Labels. Only visible labels can be selected this way. When you are done, switch the filter back if you want to select other node types; otherwise, clicks in the Viewport may target labels when you intended to work with atoms or residues.
For a consistent appearance, the default font for labels without a directly specified font is controlled in Preferences > Rendering > Labels. You can change the font for selected labels in the Inspector, or reset a label’s font by double-clicking its Font setting. Label colors can also be changed or reset, and transparency can be adjusted in the Inspector. For measurement labels, the same preferences include the number of decimal places shown for angles and distances.
A practical check before sharing a molecular scene: confirm that labels are attached to the intended structural level, inspect them at more than one zoom level, and make sure moving or selecting labels has not left the Selection filter in an unexpected state. For the full walkthrough, see the SAMSON labeling documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.