Whether you’re analyzing protein-ligand interactions or checking geometry optimization results, measuring precise atomic distances is a routine—but vital—task in molecular modeling. Yet, for many users, keeping track of those measurements or quickly accessing the most relevant ones can be frustrating or inefficient. In SAMSON, the Measure editor solves this by providing a simple but powerful way to measure and save distances directly in your workspace.
Instead of wondering about the bond length between two atoms or eyeballing distances in a complex molecular assembly, you can explicitly display and label the values you care about. Here’s how it works, and why it could streamline your daily modeling tasks.
Interactive Distance Measurement 🧪
To measure the distance between two atoms in SAMSON:
- Activate the Measure editor from the left-side menu or press Ctrl/Cmd + M.
- Click on the two atoms you’re interested in.
This will immediately display the distance between them, either temporarily or permanently (when saved as a label). Displayed measurements behave just like molecular annotations: they’re stable, visible even at different zoom levels, and easy to manage.
Labels: Temporary or Saved?
If you simply click two atoms, the resulting measurement acts as a temporary overlay. It’s always visible regardless of zoom level, but it disappears when you make your next measurement. If you want to keep multiple measurements visible, make sure to save them by hitting Enter. This turns the measurement into a label within your molecular document. Once saved, it becomes a part of your simulation session history and will be retained even after closing and reopening your file (as long as you save your project in a .sam or .samx file).
Inspect and Customize
Measurements saved as labels can be customized via the Inspector panel. For example, when measuring the distance between two atoms, additional projection values on different planes are also made available:
- XY, YZ, and XZ plane projections
- Access to the participating atoms
This is particularly useful in structural biology or materials science: separating motion or deformation along specific axes helps in interpretation and validation steps.
Visual Appearance Matters
Labels are more than just numbers; they can be stylized for clarity. You can change:
- Font and size
- Text and line colors
- Angle or plane color (for label types beyond distances)
To revert to default colors, just double-click the text element in the Inspector, or use the X button beside the color field to erase customizations.
Updating Automatically While Modeling
One of the most convenient features is automatic label updating. Measurements reflect updates due to structural movement, minimization, or interactive editing. If you move an atom using a Move editor, or reoptimize a conformation, the distance value in your label updates automatically.
Why This Matters
Having reliable and customizable distance measurements, with the option to store or discard them, can significantly improve your modeling workflow. This allows for better reporting, clearer communication, and organized inspection of molecular systems—without switching tools or manually recalculating anything.
To learn more about measurements in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.