Building Carbon Nanotubes by Hand in SAMSON: A Visual Approach to Mastering Patterns

Creating custom carbon nanotube structures can be a time-consuming and repetitive task, especially when modeling them atom-by-atom. Fortunately, with the integrated pattern editors in SAMSON, you can build nanotubes from scratch in just a few steps — while staying in full control of the molecular geometry.

This guide walks through the hands-on construction process using SAMSON’s Circular and Linear Pattern Editors. This approach is useful for molecular modelers who need tailored architectures beyond what nanotube generators can offer.

Why build manually?

Automated nanotube builders may not offer the flexibility needed to:

  • Integrate non-standard rings or molecules
  • Introduce irregular pitch or spacing
  • Optimize bonding between repeated monomers

That’s where SAMSON’s duplicating pattern editors come in: you decide what to repeat and how.

Step-by-step: From ring to tube

  1. Create your initial ring fragment. You can build a ring manually using SAMSON’s molecular editors, or use the built-in ring templates. For bonding purposes, remove hydrogen atoms on connection points and rotate to align flat.
  2. Use the Circular Pattern Editor (W shortcut) to generate a full ring from your fragment:
    • Set the number of copied instances (e.g., 12) to complete a loop.
    • Adjust the radius of the pattern to match bonding distance across fragments.
    • Click the central widget to enter values manually, if needed.
    • Click Accept to generate the ring with merged atoms.
  3. Align the ring to a known plane (e.g., XY) using the menu: Edit > Align. This will simplify orientation for tube stacking.
  4. Use the Linear Pattern Editor (L shortcut) to replicate the ring along the desired axis:
    • Translate along the Z-axis using the widget handles (e.g., 2 Å between rings).
    • If needed, apply a small rotation increment for helical nanotubes.
    • Accept to build the tube structure.
  5. Run a geometry minimization to relax any strain and optionally re-add hydrogen atoms to satisfy valences.

This process allows for high control over geometry while being visually intuitive. If you’re building more complex systems (doped rings, alternating units, etc.) these steps make it easier to prototype nanoarchitectures beyond regular carbon tubes.

Visual result

Interactive tutorial in SAMSON

Learn more

For more information on how to use pattern editors, widget controls, snapping, and options for merging atoms or grouping results, check the official SAMSON documentation page on Creating Patterns.

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

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