Visualizing molecular measurements—like distances, angles, or torsions—plays a vital role when modeling or analyzing molecular structures. Often, you’re examining multiple interactions simultaneously, especially when comparing conformers or tracking structural changes during simulations. But how do you avoid clutter while maintaining clarity? In SAMSON, the Measure editor provides a practical workflow for displaying and saving measurements through temporary and persistent labels.
Understanding the distinction between temporary and persistent labels will save time and help prevent accidental loss of important data—as some molecular modelers may have already discovered when a measurement mysteriously disappears after a few clicks.
Temporary Measurements: Fast but Fleeting
By simply activating the Measure editor (use Ctrl/Cmd + M), you can click atoms and bonds to display:
- Bond lengths (click on a bond)
- Distances between atoms (click on 2 atoms)
- Angles (click on 3 atoms)
- Torsions (click on 4 atoms)
These visuals appear immediately in the viewport, no confirmation needed. But there’s a catch: only one temporary measurement can be shown at a time. Create a new measurement, and the previous one vanishes. This behavior is intentional, making temporary measurements ideal for quick checks or exploratory modeling.
Temporary measurements are always visible regardless of zoom level, but they’re inherently volatile. If you’re adjusting atoms and redoing measurements frequently during a modeling session, it’s easy to forget what you already measured.
Persistent Labels: Save and Organize Measurements
To keep a measurement permanently within your SAMSON document, press Enter immediately after creating it. This saves it as a label. From that point on, the measurement behaves like any other label—its visibility depends on zoom, and you can customize its appearance.
Persistent labels appear in the Inspector, where you’ll be able to see associated atoms and projection information for atom-atom distances. This is particularly useful during energy minimizations or when following the effects of conformational change, since measurements automatically update as atoms move.
Tip: Use Labels Strategically
If you’re setting up multiple frames or monitoring interactions among several atoms, saving measurements as persistent labels is often the better choice. This allows you to:
- Create multiple concurrent measurements
- Inspect and manage them in the Inspector
- Export them with your project using
.samor.samxfiles
To support visual clarity, SAMSON also lets you customize label appearance (font, text color, line color, angle plane color, etc.), either per-label via the Inspector or globally via the Preferences panel.
In sum, use temporary measurements for quick feedback, but save important ones as labels if you want your measurements to persist, be reviewed, or shared.
To learn more about how to use measurement labels in SAMSON, visit the full documentation: https://documentation.samson-connect.net/users/latest/measuring/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.