A distance or angle can look obvious in a molecular structure—until you need to report it, compare it after a change, or find it again later. A measurement that exists only on screen is easy to lose. In SAMSON, the Measure editor lets you measure bonds, atom-to-atom distances, angles, and torsions, then save measurements as labels in the document when you need them to persist.
Choose the measurement that matches the question
Open the Measure editor from the left-side menu in the viewport, or use Ctrl+M on Windows/Linux or Cmd+M on macOS. Then click the structural elements needed for the measurement:
- Click a bond to show or hide its length.
- Click two atoms to measure the distance between them.
- Click three atoms to measure an angle.
- Click four atoms to measure a torsion.
This makes the editor useful for questions at different scales: a bond length, the separation between two atoms, the angle defined by three atoms, or a torsion across four atoms. The key practical step is to identify the atoms you want to examine before clicking, especially when several nearby atoms could be plausible choices.
Temporary or saved? Make the choice deliberately
A new measurement is temporary unless you save it. A temporary measurement remains visible regardless of zoom level, but the next measurement replaces it. That is handy for a quick check while exploring a structure. If you need to keep several measurements visible, press Enter after creating each one. SAMSON saves it as a label in the document, so you can retain multiple annotations rather than replacing the previous one.
Saved measurement labels behave like other labels: their visibility can depend on zoom level, and their font, color, and offset can be adjusted. If you save the document in SAMSON’s .sam or .samx format, measurement labels are saved with it. This distinction helps avoid a common workflow problem: assuming a useful on-screen measurement will still be there after moving on or reopening the document.
Let measurements follow structural changes
Saved measurements are not merely static text. When their associated atoms change position, measurements update automatically in the viewport, Document view, and Inspector. This is useful while moving atoms or carrying out interactive minimization: you can watch a measured distance or angle change as the structure changes, instead of repeatedly recreating the annotation.
For a saved label, select it and open the Inspector to see the atoms associated with the measurement. Atom-to-atom distance labels also show additional measurements for projections on planes in the Inspector. That gives you a way to inspect more than the displayed distance when you are examining a geometric relationship.
Make annotations readable, not distracting
When many labels compete for attention, legibility matters. You can adjust a saved label’s font, color, and offset, and change the colors of distance lines and angle planes in the Inspector. If a color change is no longer useful, the Inspector provides ways to return to defaults: double-click the relevant line or angle color entry, or use the clear button beside Text color to reset the text color. You can also set a font for an individual label in the Inspector.
For labels without an individually specified font, preferences under Preferences > Rendering > Labels control the font. Those preferences also let you change the number of decimal places used for angles and distances created with the Measure editor. Choosing precision that fits the task can make a figure or working view easier to read without changing the underlying structure.
A simple habit makes measurements easier to trust later: use temporary measurements for one-off checks, press Enter for anything you want to preserve, and save the document in a SAMSON format when you need the labels stored with it. For complete details, see the SAMSON measuring documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.