One of the most common frustrations molecular modelers face when analyzing molecular structures is the accidental loss of measurements between atoms. Whether you’re checking hydrogen bond lengths, backbone distances, or tracking how structures change during simulations, a single misclick can wipe out a temporary measurement. If this sounds familiar, you’re not alone—and there’s an easy fix in SAMSON.
SAMSON offers a robust Measure editor that can help you measure—not just visualize—interatomic distances, bond lengths, angles, and dihedrals. But unless you save those measurements explicitly, they’ll disappear once you start a new one. This blog post shows you how to store measurements as persistent labels—and why you might want to.
From Temporary to Persistent
By default, measurements you create in the SAMSON viewport (accessible via Ctrl/Cmd + M) are temporary. They hover conveniently in view regardless of zoom level, but the moment you click another atom to measure something else, the current one disappears.
To make a measurement permanent, simply press Enter after creating it. That’s it. It’s now saved as a label in your document. Saved measurements will stay with your project—and you won’t need to redo a distance every time you come back to a structure.
Why Save Measurements?
Saved labels come with several advantages:
- You can track changes during simulations or interactive minimizations. Labels automatically update as atoms move.
- You can customize their appearance: color, font, label offset, and even the color of lines or planes representing angles.
- You can organize and inspect your labels using the document view or the Inspector.
- Measurements will be included when you save your project using the
.samor.samxfile formats. - You can associate the label with a formal or partial charge for selected atoms using the Label editor menu.
Here’s an example of a formal charge label being added:
Dig Into the Inspector
Once a label is saved, selecting it and opening the Inspector reveals more details, particularly for distance measurements. You’ll find projections on planes, additional descriptors, and customization settings.
Customization Options
You don’t have to settle for default formatting. Customize label text, distance lines, and even torsion angles using color settings inside the Inspector:
Need to reset? Double-click the color setting to revert to default or click the X button next to the text color icon:
Bonus Tip: Change Global Preferences
You can also set global defaults for label font and the number of decimal places shown using the Preferences panel under Rendering > Labels.
In short: If you ever lost a measurement by accident, the solution is simple—just press Enter after measuring, and gain full control over those values.
Learn more about measuring 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 from https://www.samson-connect.net.