A measurement can answer a quick question—how far apart are two atoms?—but in molecular modeling, the useful question often comes next: what happens to that distance when the structure changes? A temporary readout is easy to lose, and a number without its associated atoms can be hard to interpret later. In SAMSON, you can turn measurements into document labels so they remain available as the model changes and can be inspected afterward.
Choose the measurement by the number of atoms
Activate the Measure editor from the left-side viewport menu, or use Ctrl+M on Windows/Linux or Cmd+M on macOS. Then choose the atoms relevant to the question you want to answer:
- Click a bond to show its length.
- Click two atoms to show their distance.
- Click three atoms to show the angle between them.
- Click four atoms to show the torsion between them.
This gives you a quick way to check local geometry without first building a separate annotation. For example, a two-atom distance can help you monitor a contact, while a three- or four-atom measurement describes a local angle or torsion.
Keep the reading attached to the model
By default, the displayed measurement is temporary. It remains visible at different zoom levels, but disappears when you make another measurement. Only one temporary measurement can be shown at a time. If you want to keep a reading alongside other annotations, press Enter to save it as a label in the document.
This small step changes the measurement from a transient display into a record you can return to. It is especially useful when comparing several parts of a structure, preparing a visual explanation, or keeping track of geometry during an editing session. A saved measurement label can be selected later; open the Inspector to see the atoms associated with it. For an atom-to-atom distance label, the Inspector also displays additional measurements for projections on planes.
Saved labels behave like other labels in the document: their visibility can vary with zoom, and their font, color, and offset can be adjusted. You can also change the colors of distance lines and angle planes in the Inspector. If you want a saved reading to survive a save-and-reopen workflow, save the document in a SAMSON format (.sam or .samx); measurement labels are saved with it.
Use measurements to follow structural changes
A saved measurement is not just a snapshot of a number. Measurements update automatically when their associated atoms change position or charge. That means a label can help you follow a geometric change while using Move editors or interactive minimization, rather than requiring you to repeatedly measure the same atoms by hand.
For a practical workflow, first identify the atoms and measure the geometry you care about. Press Enter if you want to retain the label. Then make the structural change and watch the measurement update. If you need multiple readings, save each one as a label instead of relying on the single temporary measurement. This makes it easier to distinguish a changing value from a reading that was simply replaced.
Make the annotation readable
For saved labels, use the Inspector to adjust label properties, including font and the colors of measurement lines or planes. You can reset a line or angle color by double-clicking its associated color entry in the Inspector; use the clear button next to Text color to reset that setting. For labels without an individually specified font, you can set a default font in Preferences > Rendering > Labels. The same preferences include the number of decimal places shown for angles and distances created with the Measure editor.
These display choices matter when a measurement is part of a busy molecular view: choose enough precision for the comparison you need, and use styling to make the annotation legible without obscuring the structure.
For the complete instructions, see the SAMSON measuring documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.