When building or analyzing molecular systems, clear communication of what you’re looking at is critical. Labels—whether it’s atom names, residue identifiers, or calculated measurements—can offer essential context. But when everything is labeled all at once, the screen quickly gets cluttered. On the other hand, disabling labels entirely can leave you feeling lost in a sea of atoms.
Striking a balance is key, and that’s where SAMSON’s label visibility tools step in. Here’s how they help you fine-tune exactly when and where your labels appear, whether you’re zoomed into an active site or exploring an entire protein complex.
The Zoom-Sensitive Visibility Mechanism
Labels in SAMSON adjust dynamically with your zoom level. Unlike static overlays, this intelligent feature ensures that only relevant labels are displayed depending on how close you are to the model. For example:
- Zooming in reveals labels for finer structural units such as atoms or bonds.
- Zooming out fades those out in favor of higher-level components like residues or entire molecules.
This makes the visualization significantly more manageable and keeps your workspace readable—no matter what level of detail you’re working at.
Manual Control Over Visibility
For workflows that demand more control, SAMSON offers manual customization of label display thresholds. You can choose to override the default zoom behavior and set specific visibility ranges for each label by adjusting two parameters:
- Minimum display radius
- Maximum display radius
To do this, select a label and open the Inspector panel. There, you’ll find numeric fields for both parameters—you can adjust them to suit your visual needs. A smaller display radius makes the label appear only when zoomed quite close, while a larger one ensures it remains visible even from a distance. This allows you to, for instance, keep an important marker visible at all times while letting less critical annotations fade away when zooming out.
Show or Hide Labels as Needed
Sometimes, labels may get in the way or simply aren’t needed. Turning them off temporarily is easy using the Document view. Just tick or untick the checkboxes next to each label or group of labels to toggle visibility.
Visual Transition Demo
Here’s an example of how labels transition with zoom. This GIF illustrates how label visibility automatically changes as you move closer to or away from the model:
Why Care About Label Visibility?
When preparing figures for presentations, publications, or just trying to get a clearer understanding of molecular interactions, label clutter can be a major problem. Controlling label visibility can help you highlight what’s important and avoid misleading or confusing visuals.
Similarly, during collaborative work, automatic zoom-based transitions reduce the need for repeated manual toggling, allowing everyone to explore the system more naturally and comfortably.
Wrapping Up
Effective molecular modeling isn’t just about putting atoms together—it’s also about visual storytelling. With SAMSON’s flexible and intuitive label visibility controls, you can keep your focus sharp and your screen clutter-free.
To learn more, visit the full documentation page on Labeling in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at samson-connect.net.