Using Pattern Editors to Build Custom Nanotubes Without Scripting

Constructing nanotubes manually can be a tedious and error-prone process for molecular modelers. Aligning rings, duplicating atoms, merging structures, and optimizing geometry often requires significant time and care—especially if relying on custom scripts. In this post, we’ll show an alternative approach using SAMSON’s built-in Pattern Editors to construct custom nanotubes visually and interactively, without any scripting.

Why manual nanotube design matters

While there are tools that generate predefined nanotube geometries, researchers often need more control: perhaps to model a defect, alter repeat distances, align rings differently, or build only a section of a tube. Manual creation allows flexibility—but it must be efficient and reproducible.

What you’ll use

  • Circular Pattern Editor (W): to create a single carbon ring or layer of the tube.
  • Linear Pattern Editor (L): to replicate along the tube’s axis.
  • The Edit > Align menu: for positioning and orientation before stacking.
  • Optional: Geometry optimization to clean up the resulting structure.

Step-by-step: building the tube

  1. Create a carbon ring manually (e.g., a 6-membered carbon ring), and remove hydrogens. Make sure atoms are roughly in-plane and edges can connect.
  2. Rotate the ring in the viewport to align with the XY plane. SAMSON’s viewport tools or Edit > Align help with this.
  3. Use the Circular Pattern Editor (W) to create a closed loop:
    • Use 12 or more copies depending on desired tube diameter.
    • Adjust radius to ensure atoms touch just enough to bond.
    • Click Accept to finalize the ring.
  4. Align the plane precisely if needed using Edit > Align.
  5. Use the Linear Pattern Editor (L) to duplicate the ring along the Z-axis:
    • Set translation distance (e.g., 2 Å or whatever fits your bonding geometry).
    • Use the mouse wheel or precise input to control the number of layers.
    • Optionally rotate each copy incrementally to twist the tube.
    • Click Accept when done.
  6. Minimize geometry (via the Minimization Controller) to allow atoms to relax into stable bonds.

Tips

  • To merge overlapping atoms, enable “Automatically merge nearby atoms” in Preferences > Edit for your active Pattern Editor.
  • If you’re not happy with a pattern, undo and reapply with new parameters—it’s fast and visual.
  • Use snapping to control spacings during duplication.

This approach is ideal when you want to explore custom geometries interactively—perfect for teaching, prototyping, or preparing input for more detailed simulations.

Learn more in the detailed documentation example for constructing a nanotube manually.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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