A distance or angle can look clear in a static structure, then become difficult to track as soon as you start moving atoms or refining the model. Repeating measurements by eye is slow, and a temporary annotation can disappear just when you need to compare it. SAMSON’s Measure editor helps you check molecular geometry directly in the viewport—and keep saved measurements connected to the atoms they describe.
Measure the geometry you need
Open the Measure editor from the left-side viewport menu, or use Ctrl+M on Windows/Linux or Cmd+M on macOS. Then click the relevant feature or atoms:
- Click a bond to toggle its displayed length.
- Click two atoms to measure their distance.
- Click three atoms to measure an angle.
- Click four atoms to measure a torsion.
This gives you a practical way to inspect local geometry without needing to estimate it from the screen. For example, you can check a bond length, examine the angle formed by three atoms, or inspect a torsion across four atoms while working on a structure.
Temporary check or saved annotation?
A measurement remains temporary unless you save it as a label. Temporary measurements stay visible at any zoom level, but only one temporary measurement can be shown at a time: making another measurement replaces the previous one. That makes the temporary display handy for a quick check, but less suitable when you want to preserve several measurements for later review.
To keep a measurement, press Enter. It is saved as a label in the document. You can then retain multiple measurement annotations instead of replacing one with the next. If you save the document in a SAMSON format (.sam or .samx), labels containing measurements are saved with it.
Follow a measurement as atoms move
A saved measurement is not just a number captured at one moment. When its associated atoms change position, the measurement updates automatically in the viewport, Document view, and Inspector. Measurements also update when associated atoms change their charges. This is useful when moving atoms or performing interactive minimization: you can watch the value change as the structure changes, rather than taking a series of disconnected snapshots.
Inspect what a saved measurement refers to
If you need to identify the atoms behind an annotation, select the saved label and open the Inspector. The Inspector shows the measurement information and provides access to the atoms associated with it. A saved atom-to-atom distance label also includes additional measurements for projections on planes, which can help when a distance needs to be considered in relation to a plane.
Make annotations easier to read
Saved measurement labels follow the behavior of other labels: their visibility depends on zoom level, and you can adjust their font, color, and offset. In the Inspector, you can also change the color of distance lines and angle planes. If you want to restore a measurement line or angle color, double-click its associated text in the Inspector. To reset the text color, use the clear button next to Text color.
For consistent annotations across a document, preferences let you choose the font for labels that do not have an individually specified font. You can also set how many decimal places are shown for distances and angles created with the Measure editor. This can make a set of measurements easier to scan without changing the underlying structure.
For a quick, disposable check, use a temporary measurement. For comparisons you want to keep while editing or share in a saved structure, press Enter to turn it into a label. Read more in the SAMSON measuring documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.