Duplicating Molecular Structures Without the Mess: Mastering Pattern Editors in SAMSON

In molecular modeling, creating and analyzing complex architectures often starts with simple structural units. But when it comes to replicating molecular motifs—be it for nanotubes, molecular crystals, or repeating protein units—the process can be surprisingly tedious. If you’ve ever spent too much time duplicating molecules manually and adjusting them one by one, you’re certainly not alone.

This is where SAMSON’s Pattern Editors provide a useful alternative. These tools allow for fast, visual, and precise replication of molecular fragments using linear, circular, or curved patterns. Whether you’re working in nanotechnology or biomolecular modeling, learning how to use these editors can significantly reduce repetitive interactions and streamline structure construction.

What Are Pattern Editors?

SAMSON includes three pattern building editors:

  • Linear Pattern Editor: best for polymers, DNA, or nanotubes.
  • Circular Pattern Editor: ideal for ring structures or assembling symmetrical units.
  • Curved Pattern Editor: versatile for modeling non-uniform bending structures.

Each editor provides interactive widgets that let users duplicate selected structures while controlling position, orientation, and repetition—all in a live, visual environment.

Common Scenario: Building a Nanotube

Let’s walk through a common use case where these tools shine: manually constructing a carbon nanotube.

  1. Create a benzene-like ring and remove hydrogen atoms. Rotate the structure to align edges. This forms the base unit for the tube.
  2. Use the Circular Pattern Editor (W key):
    • Set the number of instances (e.g., 12) to complete a circle.
    • Adjust the radius to close chemical bonds and click Accept.
  3. Align the ring to a plane using Edit > Align.
  4. Use the Linear Pattern Editor (L key):
    • Set a Z-translation value (e.g., 2 Å) and adjust the number of stacked rings.
    • Make fine rotational tweaks if needed.
    • Click Accept to form the nanotube structure.
  5. Optional: Minimize the structure and re-add hydrogen atoms.

This method is not limited to nanotubes—it translates easily to other repeating systems like amyloid fibrils, nanorings, or even DNA helices when paired with curved patterns.

Fine-Tuning with Preferences

In the preferences menu (Edit > Preferences > Edit), each pattern type exposes additional options:

  • Merge nearby atoms automatically.
  • Adjust hydrogen atoms based on geometry.
  • Group generated structures or merge them with the original.

Combining these with alignment and distribution tools (Edit > Align / Distribute) gives you fine control over how your molecular systems are arranged spatially.

Quick Tips to Get Started

  • Use Ctrl + scroll (or Cmd + scroll on macOS) to quickly adjust the number of copies.
  • Click widget centers to type exact translation/rotation values.
  • Leverage the interactive previews before committing your design.

Pattern Editors are part of what makes SAMSON an efficient environment for molecular design. If you’re still manually duplicating atoms or struggling with structural symmetry, these editors could be your next timesaver.

Interactive tutorial in SAMSON

To learn more about building patterns 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.

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