In molecular modeling, clarity is key. Whether you’re preparing figures for publication, sharing interactive models, or simply analyzing a complex system, being able to label and annotate atoms, residues, or molecules is essential. However, many users of SAMSON—the integrative molecular design platform—may initially run into a subtle but important issue: labels sometimes disappear when zooming in or out.
This isn’t a bug—it’s actually a feature. SAMSON automatically adjusts label visibility based on zoom level so that your screen isn’t overloaded with information. But how does it work, and how can you control which labels appear and when? In this post, we’ll take a look at label visibility in SAMSON and how you can use it effectively in your workflow.
Why labels change when you zoom
Labels in SAMSON are set to become visible or invisible based on the zoom level in the Viewport. When zooming out, labels associated with smaller structures (like atoms) begin to disappear, while those linked to larger structures (such as entire molecules) remain or appear. Conversely, when zooming in, atomic-level labels become visible again.
This helps avoid visual clutter when you’re viewing an entire protein or molecular complex—SAMSON prioritizes readable labels depending on the level of detail you’re focusing on.
Controlling label visibility manually
If you want finer control over when labels are shown, SAMSON allows you to define the label’s visibility range through its display radius settings.
To do this:
- Select the label(s) you want to adjust.
- Open the Inspector panel.
- Find the fields for Minimum display radius and Maximum display radius.
- Enter the zoom radius range within which the label should be visible.
With this approach, you can ensure crucial annotations remain visible when needed—whether you’re zoomed into a protein’s active site or viewing the entire macromolecule.
Quick switch: turning labels on or off
You can also quickly switch label visibility on or off manually:
- In the Document view, simply tick or untick a label to show or hide it.
This is useful when you want to momentarily remove annotations without deleting them or altering their display settings.
Putting it all together
Understanding how and when labels appear in SAMSON allows you to stay in control of your molecular representations. Whether you’re labeling key residues in an enzyme, assigning unique names to ligands, or noting experimental distances, label visibility helps you adapt the visual output to your audience and your goals.
Want to highlight secondary structure elements only when zoomed out? Now you can. Need atom-by-atom labels that only show up when zoomed close? Now it’s just a setting away.
To learn more about labels and how to manage them in SAMSON, visit the official documentation here: https://documentation.samson-connect.net/users/latest/labeling/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.