A measurement can answer a simple but important question: are these atoms still the right distance apart? The challenge is that molecular structures change as you move atoms or run an interactive minimization. A number that was correct a moment ago may no longer describe the current geometry—and a temporary annotation can disappear when you make another measurement.
SAMSON’s Measure editor helps address both problems. It measures bond lengths, distances, angles, and torsions directly on the structure, and saved measurement labels update when their associated atoms move. Here is a practical way to use it without losing track of what you measured.
Choose the measurement by the number of atoms
Open the Measure editor from the left-side menu in the viewport, or use Ctrl/Cmd + M. Then click the relevant part of the structure:
- Click a bond to show its length.
- Click two atoms to show their distance.
- Click three atoms to show the angle.
- Click four atoms to show the torsion.
This makes it easy to check a specific geometric feature while keeping the structure visible. For example, a distance measurement can help you monitor a pair of atoms, while an angle or torsion measurement describes the geometry defined by three or four atoms.
Temporary for a quick check; saved for ongoing work
By default, a measurement is temporary. It remains visible regardless of zoom level, which is useful when you need a quick readout. But there can only be one temporary measurement: creating another replaces the previous one.
If you want to keep several measurements in your document, press Enter after creating each one. This saves it as a label. Unlike a temporary measurement, a saved label follows label visibility behavior, including changes with zoom level. If you save the document in SAMSON’s .sam or .samx format, measurement labels are saved with it.
A useful habit is to treat temporary measurements as scratch work and save the ones you expect to revisit. That keeps a quick inspection uncluttered while preserving important checks for later.
Keep measurements meaningful while the structure changes
Saved measurements update automatically when their associated atoms change position. This means you can keep a distance, angle, or torsion in view while using Move editors or interactive minimization, rather than repeatedly measuring from scratch. The updated values are shown in the viewport, Document view, and Inspector.
That can make an annotation a useful part of an editing workflow: it records which atoms you are monitoring and continues to report their relationship as the structure changes. For a saved label, select it and open the Inspector to access the atoms associated with the measurement. Saved atom-to-atom distance labels also provide additional measurements for projections on planes in the Inspector.
Make saved measurements readable
When a label is part of a busy view, its appearance can matter as much as its value. Measurement labels can be formatted like other labels: you can adjust font, color, and offset. In the Inspector, distance lines and angle planes have their own color settings. If you change a line or angle color and want to restore its default, double-click the associated text in the Inspector. To reset a label’s text color, use the clear button next to Text color.
You can set a font for an individual label in the Inspector. For labels without an individually specified font, use Preferences > Rendering > Labels. Those preferences also let you change the number of decimal places used for angles and distances created with the Measure editor. Choose precision that makes the value easy to interpret without implying more certainty than your analysis needs.
In short: measure the geometry you need, press Enter to keep important annotations, and let saved measurements track the atoms as you edit. For full details, see the SAMSON measuring documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.