Speeding up Nanotube Design with Pattern Editors in SAMSON

For molecular modelers working on nanostructures, building carbon nanotubes and similar architectures atom by atom is time-consuming and error-prone. Small misalignments between atoms can create structurally incoherent models and increase the time required for cleanup and minimization. If your work regularly involves designing nanoscale systems like carbon nanotubes, there’s a more efficient way using SAMSON’s Pattern Editors.

In SAMSON, the Circular and Linear Pattern Editors make it easier to construct organized, symmetrical tube-like structures—such as CNTs—from fundamental building blocks. Let’s walk through the process and show how SAMSON helps reduce the effort, so you can focus on design rather than manual replication.

Step-by-Step: Building a Nanotube in Minutes

Here’s a workflow using the pattern builders to construct a simplified carbon nanotube. The same concepts apply when building other periodic nanostructures too:

  1. Create a base ring, such as a hexagonal carbon ring. Remove hydrogens and rotate the fragment to align its edges with the X or Y axis.
  2. Apply the Circular Pattern Editor (shortcut: W) to replicate the ring:
    • Increase the instance count (e.g., 12) to complete the loop.
    • Dynamically adjust the radius so that edge atoms of neighboring rings are close enough to bond.
    • This step produces a closed molecular ring representing the cross-section of your tube.
  3. Align the ring with the XY plane using Edit > Align commands, enabling the next step to replicate along a consistent axis.
  4. Use the Linear Pattern Editor (shortcut: L) to stack the ring:
    • Translate copies along the Z-axis to create the tube length (e.g., every 2 Å).
    • Apply any incremental rotation if your design requires helical structures.
    • Accept the pattern, and atoms that are close enough will merge automatically.
  5. Use Minimization to relax the tube and add hydrogens, if needed.

This combination of circular and linear duplication transforms a process that would otherwise involve dozens of manual repetitions into a structured, visual experience with interactive drag handles and real-time feedback.

Why It Matters

Nanoscale architectures often depend on high symmetry and precise spacing. Using Pattern Editors ensures consistent geometry across the design while allowing fine-tuned rotations and translations. This is a practical solution for researchers working on:

  • Carbon nanostructures (nanotubes, fullerenes)
  • Periodic biomolecular assemblies
  • Crystal-like arrangements in materials science

Details like snapping, rotation control, and atom merging settings can be adjusted globally under Preferences > Edit > Create pattern to fit your project’s constraints.

Visual Guide

This screenshot from the SAMSON documentation shows an interactive tutorial when working with atoms in the builder module:

Interactive tutorial in SAMSON

To further refine or align your structure, make use of the Align & Distribute tools found under the Edit menu, which help maintain consistency across large assemblies.

Conclusion

If you’ve spent hours replicating molecular structures manually, the Pattern Editors in SAMSON offer a powerful alternative. Whether you are designing nanodevices or modeling advanced materials, these tools bring structure and speed to your workflow—without sacrificing control or precision.

To learn more, visit the original documentation on Creating Patterns in SAMSON.

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

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