When performing molecular modeling, there are moments when a single distance or angle carries more meaning than lines of code. Whether you’re comparing bond lengths between minimized geometries, analyzing conformational changes, or just trying to keep track of a torsion across different frames, visual clarity plays a big role in your decision-making.
The challenge? Temporary measurements made during an analysis often vanish before you’re ready—making it hard to track multiple metrics at once or revisit your findings later. Fortunately, in SAMSON, there’s a simple, yet powerful way to turn temporary insights into persistent annotations: measurement labels.
From Temporary to Trackable
SAMSON’s Measure editor lets you quickly click on atoms to display:
- Bond lengths (click on a bond)
- Distances between atoms (select two atoms)
- Angles (three atoms)
- Torsions (four atoms)
But these measurements by default are temporary: only one at a time is shown, and it disappears when a new one is made. To preserve a measurement, simply press Enter. This saves it as a label in your molecule’s document, meaning it becomes part of your project and can be recalled, modified, or exported.
Why Labels Matter in Molecular Workflows
Here’s why saving your measurements as labels can make a difference:
- Consistency: Labels are automatically updated when the geometry changes—for example, when you move atoms or perform an energy minimization.
- Comparison: You can save multiple measurements at once and compare them without redoing steps.
- Data reuse: Labels are saved with .sam or .samx files, so you won’t lose analytical annotations when reopening your project later.
- Accessibility: You can always inspect the labeled atoms using the Inspector and even access projections, like distance components on molecular planes.
Make It Yours: Customizing Label Appearance
Once saved, these labels aren’t static—they’re customizable:
- Use the Inspector to change text color, line colors (for distances), and angle plane coloring.
- Modify the label font for individual labels or set defaults for your entire document in Preferences > Rendering > Labels.
- Reset colors easily by double-clicking or using the clear button shown below.
The number of decimal places for angles and distances can also be adjusted in your Preferences panel—especially useful for high-precision modeling work.
Adding Charges as Labels
Need to annotate atomic charges visually? SAMSON also allows you to add formal or partial atomic charge labels using the context toolbar:
This creates a more complete picture—literal and analytical—of your molecular model.
Conclusion
By treating your measurements as persistent, customizable labels, you’ll be able to build models that are not just visual representations but also annotated stories of molecular interactions. It’s a small habit that helps you avoid rework and offers more clarity when analyzing or sharing your models.
To learn more about measurements in SAMSON, visit 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 get SAMSON at https://www.samson-connect.net.