A distance measured on a static molecular structure is easy to record. The harder problem comes next: after you move atoms or run an interactive minimization, is that number still accurate? Repeating measurements by hand interrupts the modeling workflow and makes it harder to compare the structure with the quantity you are trying to monitor.
In SAMSON, measurements can stay associated with the atoms they describe. When those atoms change position, saved measurements update automatically in the Viewport, Document view, and Inspector. This makes a measurement useful not just as a snapshot, but as a value you can follow while editing a structure.
Choose the measurement that matches the question
The Measure editor is available from the left-side menu in the Viewport, or with Ctrl/Cmd + M. The number of atoms you click determines the geometric quantity:
- Click a bond to toggle its length.
- Click two atoms to measure the distance between them.
- Click three atoms to measure the angle.
- Click four atoms to measure the torsion.
That gives you a quick way to turn a structural question into something observable: how far apart are these atoms, what angle do they form, or how is this group rotated around a bond?
Temporary reading or persistent annotation?
A new measurement is temporary until you save it. It remains visible regardless of zoom, but the next measurement replaces it. That behavior is handy when you need a quick check and do not want to clutter the document with annotations.
If you want to keep a measurement while making another one, press Enter to save it as a label in the document. Saved labels remain available alongside your structure, and multiple measurements can be kept this way. If you save the document in a SAMSON format (.sam or .samx), measurement labels are saved with it.
A practical workflow is to use a temporary reading for an initial check, then save the measurements you expect to revisit. Give persistent annotations enough context to be useful later: choose measurements that answer a specific structural question, rather than labeling every possible pair of atoms.
Follow changes instead of remeasuring
Once a measurement is saved, the associated atoms remain the basis for its value. As their positions change, the displayed measurement updates. You can therefore watch a distance, angle, or torsion as you use Move editors or interactive minimization, rather than relying on a number measured before the structure changed.
This is especially useful when the aim is to observe how a local geometric relationship responds to editing. Keep the measurement visible while making a change, then inspect the updated value. The annotation provides continuity between the structure before and after the edit; it does not, by itself, explain why the geometry changed.
Inspect the saved measurement
To work with a saved measurement, select its label and open the Inspector. The Inspector shows information about the measurement and the atoms associated with it. For an atom-to-atom distance label, additional measurements for projections on planes are also available there. This can help when a single straight-line distance is not the only geometric detail you want to examine.
Saved measurements behave like other labels: their visibility can depend on zoom, and their font, color, and offset can be adjusted. The Inspector also lets you change the colors of distance lines and angle planes. If you want to restore a line or angle color to its default, double-click the corresponding text in the Inspector. To reset text color, use the clear button next to Text color.
For a consistent display across labels, you can set a font in Preferences > Rendering > Labels for labels without an individually specified font. That area also controls the number of decimal places shown for angles and distances created with the Measure editor. Adjusting precision can make annotations easier to read without changing the underlying structure.
The main benefit is a simpler feedback loop: measure a relationship, save it if you need to keep it, and let the annotation follow the atoms as the model changes. For the full guide to measurements and their appearance settings, see the SAMSON Measuring documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.