One of the common challenges molecular modelers face while working with complex systems is organizing and labeling structures effectively—especially when visualizing large biomolecules at different scales. Labels help annotate key atoms, residues, or molecular entities, but there’s often a problem: as you zoom in and out, labels may disappear or overlap in ways that can make visual analysis harder rather than easier.
This blog post explores a little-known but useful functionality in SAMSON: controlling the visibility of labels as a function of zoom level, using label display radii. Understanding how this works can greatly improve the clarity and effectiveness of your molecular presentations and explorations.
Why labels behave differently at different zoom levels
When visualizing molecular systems, it’s common to adjust your viewpoint to focus on different levels of detail—from a single atom to an entire molecular complex. One of SAMSON’s thoughtful design features is that label visibility adapts to your zoom level: smaller labels (for atoms) fade out as you zoom out, and labels for larger structures (like molecules) appear. Conversely, when zooming in, detail-rich labels gradually emerge.
This adaptive visibility helps reduce visual clutter, but there are situations where control is essential. You may want to keep labels visible regardless of zoom level—for example, during a presentation—or you may want a particular label to disappear sooner.
How to modify label visibility in SAMSON
Each label in SAMSON has associated minimum and maximum display radii, which define its visibility range based on your zoom level. You can modify these to fine-tune when a label should appear or disappear.
Here’s how to do it:
- Select a label by clicking on it in the Document view or directly in the Viewport (make sure your selection filter is set to “Labels”).
- Open the Inspector.
- Look for the parameters labeled Maximum display radius and Minimum display radius.
- Adjust the values accordingly:
- A lower minimum radius allows the label to appear even when you’re zoomed very close.
- A higher maximum radius enables the label to remain visible even when you zoom out far.
This control gives you flexibility depending on the scale of the system you’re visualizing. Whether you’re labeling an active site in a protein or highlighting interaction centers in a complex, meaningful visibility enhances comprehension.
Why this matters
If you’ve ever recorded a demonstration, taught a class, or shared a screen in a meeting, you’ve probably felt the frustration of a disappearing label just when you needed it most. Static label visibility doesn’t work well for all contexts, especially when spatial density and scale vary significantly across the system.
By customizing label display radii, users tailor their visualization experience. This enables clearer communication, better documentation, and more effective visual storytelling in molecular design.
Visual Example
Here’s how label visibility changes dynamically in SAMSON, and how adjusting the display radii can make a difference:
Conclusion
Adjusting the visibility range of labels using display radii in SAMSON might seem like a small trick, but it can have a big impact on how effectively you communicate and understand molecular systems visually. Take a few minutes to tweak these settings in your next session—you may be surprised by how much easier it becomes to ‘read’ your molecules.
To learn more about labeling in SAMSON, visit the full documentation here: https://documentation.samson-connect.net/users/latest/labeling/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.