Many molecular modelers have shared the same frustrating experience: measuring a distance or angle between atoms in a molecular system, only to realize that the value disappeared moments later. What’s going on here?
In SAMSON, molecular measurements like bond lengths, angles, and dihedrals can be displayed instantly using the Measure editor. It’s quick and efficient: click on a bond, two atoms, three atoms, or four atoms to view the corresponding measurement. But there’s a subtle detail that’s easy to overlook—if you don’t save the measurement, it will vanish the next time you create a new one.
This ephemeral behavior can be confusing, especially when you’re deep into analysis or preparing your structure for publication. SAMSON shows only one unsaved (temporary) measurement at a time. To preserve measurements, you need to convert them into labels in your document. You can do this easily by pressing the Enter key after a measurement is created.
Why Save as a Label?
- Persistent visualization: Labels remain visible even when you zoom, rotate, or move your model.
- Inspectable data: You can review and select associated atoms and measurements through the Inspector.
- Export safety: Labels are stored in .sam or .samx files, so saved measurements are preserved when you save your project.
How to Save a Measurement
After clicking to create a measurement — such as selecting two atoms to measure a distance — simply press Enter. That’s it. The measurement becomes a label, which can now be stylized, inspected, or deleted later. This label acts as a permanent annotation in your document.
Here’s a tip: If you create a temporary measurement and forget to press Enter, the moment you start another measurement, the previous value will disappear. So, when you record something important, make sure to save it immediately.
Visibility and Appearance
Once saved as labels, measurements gain useful properties. You can:
- Modify font size and text color
- Change line or plane colors associated with the measurement
- Set visibility according to zoom level
All of these are accessible via the Inspector. You even have options to reset colors back to defaults by double-clicking the text or clicking the X in the styling sections.
Formal and Partial Charges as Labels
Besides geometric measurements, SAMSON also lets you generate labels showing formal or partial charges of atoms. These can be added through the context toolbar:
Label > Add label to... > Atoms (formal charges)
This is especially useful when analyzing reactivity or electronic properties in your system. The labels update automatically when atom charges change, such as during interactive minimization.
A Small Step That Makes a Difference
Saving a measurement as a label might take an extra second, but it ensures your hard work is not lost. Whether you’re building molecular models, preparing teaching material, or running dynamic analyses, labeling makes sure the insights you gain are easy to track and share.
To learn more, visit the full page on measuring in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.