Easily Extend Molecular Structures with SAMSON’s Linear Pattern Editor

Creating complex molecular systems often involves the repetitive and precise placement of substructures—like repeatedly stacking rings of atoms or assembling polymers. While this can be done manually, it usually takes time and careful alignment. Fortunately, SAMSON‘s Linear Pattern Editor solves this by allowing modelers to position and replicate structures in just a few steps, significantly reducing modeling effort and errors.

In this post, we explore how the Linear Pattern Editor can accelerate your workflow and keep your models accurate and consistent—especially when creating polymers, molecular chains, or stacking repeating units for materials modeling or nanotechnology applications.

What is a Linear Pattern?

A linear pattern is a repeating arrangement of a structure along a defined direction. In molecular modeling, this might mean duplicating a monomer to model a polymer, or aligning ring-shaped structures to form a nanotube. SAMSON simplifies this with an intuitive visual tool, complete with snapping, rotation, and copy count controls.

Step-by-Step: Creating a Linear Pattern

  1. Build or load your molecule: Use SAMSON’s molecular builders or import an existing structure. For example, start with a small ring structure or a simple organic molecule.
  2. Select your structure: Use the selection tools or directly click the structure in the viewport. You can select atoms, molecules, or entire functional groups.
  3. Activate the Linear Pattern Editor: Use the shortcut L or select the editor from the editor toolbar on the left of the SAMSON viewport.
  4. Use the on-screen widget: Drag handles appear that allow you to translate and rotate your structure interactively.
  5. Set precise transformations: Hold Ctrl (or Cmd on macOS) and click on the widget to enter exact displacement values (e.g., move 2 Å along the Z-axis).
  6. Adjust copy count: Scroll the mouse wheel over the central widget to increase or decrease the number of duplicates.
  7. Accept the result: Finalize your pattern with a single click, and the editor will create the full structure with your chosen parameters.

Example: Creating a Nanotube Segment

As a practical use case, consider constructing a segment of a carbon nanotube:

  1. Create a single carbon ring, remove hydrogens, and align it to the desired plane.
  2. Use the Circular Pattern Editor (W) to form a full ring from multiple copies.
  3. Then, apply the Linear Pattern Editor (L) to stack the ring along the Z-axis and build the tube body. Adjust spacing and rotation if necessary to ensure proper bonding.

Use the Preferences panel to control behaviors like automatic atom merging or hydrogen adjustment, ensuring chemical accuracy.

Why This Matters

Whether you’re modeling biomolecular filaments, repeating lattice structures, or designing nanomachines, being able to rapidly create and fine-tune repeating components will save time and reduce the likelihood of structural errors.

With built-in visualization, snapping, and numerical input options, the Linear Pattern Editor bridges visual modeling and precision requirements—letting you focus more on your hypothesis and less on alignment work.

To explore the full scope of tools available, including the Circular and Curved Pattern Editors, visit the full documentation page here.

Interactive tutorial in SAMSON

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

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