As molecular systems grow in size and complexity, adding labels to specific atoms, residues, or molecules can be a great way to identify and present the most relevant parts of your structure. However, it’s easy for labels to become overwhelming, especially when zooming in or out, navigating large structures, or preparing images. If you’ve ever felt your screen was overloaded with too much information — or too little — understanding how label visibility works in SAMSON can make a big difference. Here’s a deep dive into how you can better control label visibility to keep your molecular models both informative and visually clear.
Labels: Useful, Until They’re Not
In SAMSON, labels are stored in your document and are shown directly in the viewport. They are commonly used to show names, groups, or measurement results. But they can quickly clutter your screen if not managed properly — especially when you’re zooming between the atomic and molecular scale.
Automatic Visibility Management
One of the subtle but powerful features of SAMSON is dynamic label visibility based on zoom level. When you zoom out, labels for smaller structures (like atoms) vanish, while labels for larger structures (like entire molecules) remain visible — and the opposite happens as you zoom in.
This behavior is particularly helpful, but it isn’t always obvious or intuitive unless you’ve interacted with it purposefully. If you’re ever wondering why a label you just added is no longer visible, zoom level might be the reason.
Manual Control with Display Radii
To decide exactly when a label should show up while zooming in and out, you can assign minimum and maximum display radii.
To do this:
- Select the label.
- Open the Inspector.
- Adjust the Minimum display radius and Maximum display radius values.
This allows you to tune visibility per-label, which is especially useful when preparing presentations or figures where you want certain information to always (or never) appear regardless of the zoom level.
Toggling Visibility in Document View
You can quickly enable or disable label visibility altogether using the Document view. Simply tick or untick the visibility checkbox next to each label. This is useful when you want to hide information temporarily without deleting anything.
Best Practices
- For large systems, use fewer, more meaningful labels at higher levels (e.g., molecules or chains), and add detailed labels (e.g., atom names) only when zoomed in locally.
- Use the display radius settings as a way to progressively introduce information as your audience zooms in while exploring the system.
- Leverage the Document view to organize your labels and enable/disable them quickly when preparing different views.
Keep Your Workspace Clear and Effective
Taking time to manage label visibility can significantly improve how you interact with your molecular structures and how others perceive them, especially in collaborative or educational settings. Whether you’re building a complex protein-ligand system or preparing figures for publication, clear labeling improves both usability and aesthetics.
To learn more about labeling in SAMSON, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.