A common challenge in molecular modeling—especially in nanotechnology and materials science—is constructing large, periodic structures like carbon nanotubes (CNTs). These structures are often composed of repeated rings or motifs, and manually placing each unit is time-consuming and error-prone.
If you’ve ever struggled with aligning hexagonal rings or creating regularly spaced patterns along an axis, SAMSON’s Pattern Editors offer a streamlined, visual workflow that significantly simplifies this task.
From rings to tubes: A guided example
Let’s walk through how to construct a CNT-like structure using SAMSON’s Circular and Linear Pattern Editors available from the Editor Toolbar or the Find everything… bar.
Step 1: Build a carbon ring
Create a basic carbon ring using atomic building tools. Remove hydrogens and rotate the ring to align its edges using the move tools.
Step 2: Form a perfect loop with the Circular Pattern Editor
- Activate the Circular Pattern Editor (shortcut: W).
- Increase the number of copies (e.g., 12) to close the loop.
- Adjust the radius visually or numerically (by Ctrl or Cmd + clicking on the center widget) so ring edges overlap.
- Click Accept to finalize and merge overlapping atoms.
Step 3: Align the ring
Use Edit > Align to place the ring on a specific plane, like the XY plane. This ensures a straight stacking path for the next step.
Step 4: Stack rings into a tube
- Activate the Linear Pattern Editor (shortcut: L).
- Set a translation distance along the Z-axis (e.g., 2 Å).
- Use Ctrl/Cmd + scroll to increase the number of copies.
- If needed, set small rotational increments to align bonds.
- Click Accept to finalize the nanotube structure.
Step 5: Optimize the structure
Once your tube is built, use the Minimize tool to relax the geometry. You can optionally add hydrogens based on pattern preferences.
Why this matters
These visual, interactive tools cut down on time previously spent on repetitive placement and adjustment tasks. Whether you’re modeling biomolecular chains, nanotubes, or other symmetrical architectures, this method supports fast prototyping and exploration.
Pattern parameters are easy to refine, and structures update in real time. You still retain full control for precise alignment and geometry tweaking.
More resources
Watch how to use the Pattern Builders in this portion of the SAMSON 2025 webinar:
To learn more, visit the official documentation page: Pattern Creation — SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.