When working with molecular systems, tracking precise physical quantities such as bond lengths and angles is essential—especially during conformational changes, docking, or real-time energy minimization. But manually updating those values as atoms move? That’s time-consuming and difficult to follow visually.
Fortunately, SAMSON has a built-in solution that automatically updates your measurements in real time as molecular structures evolve. Whether you’re repositioning atoms or running an interactive minimization, your displayed measurements—including distances, angles, torsion angles, and more—will follow every structural change and remain accurate.
Why this matters
Monitoring how structural quantities change during simulations is crucial for understanding molecular behavior. For example, how does a hydrogen bond stretch during a rotation? Does an angle approach a specific value during minimization? SAMSON’s system helps you track these parameters continuously without needing to remeasure or reannotate manually.
How it works
To enable this, use the Measure editor, accessible via the left-side toolbar in the Viewport or by pressing Ctrl/Cmd + M.
Use the following interactions to add your measurements:
- Click on a bond to toggle its length.
- Click on two atoms to display their distance.
- Click on three atoms to measure an angle.
- Click on four atoms for a torsion angle.
The measurements immediately appear in the Viewport, and remain visible even as you zoom or rotate the model. To keep a measurement across sessions or combine it with other annotations, hit Enter to save it as a label in the document.
What makes it dynamic?
Once saved, these measurement labels automatically update alongside any structural changes—whether atoms are manually moved with Move editors, or undergo conformational shifts during interactive minimization.
This dynamic behavior is available not only in the visual Viewport, but also in related interfaces like the Document view and the Inspector. That means your numerical data stays synchronized with what you see and what you analyze—without effort.
Practical example
If you’re tweaking geometry to optimize a ligand binding pose, you can keep an eye on critical distances (e.g., donor-acceptor pairs or active site contacts) throughout the process. As atoms shift, SAMSON updates the measurements in real time. Need to monitor more than one value? Simply add and save additional labels.
Helpful hint
To avoid visual clutter, keep temporary measurements when quickly exploring, and press Enter only to save key measurements. SAMSON will otherwise replace the previous one with the next measurement, keeping the interface clean and focused.
Learn more about automatic measurement updates and labeling at the official documentation page: 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.