Anyone who builds molecular systems knows how time-consuming and repetitive it can be to manually duplicate and arrange atomic units in nanoscale patterns. Whether you’re modeling a nanotube, assembling a biomolecular superstructure, or creating a mesoscopic material, controlling the arrangement of repeating units can take hours—even days—without the right tools.
That’s where the Pattern Editors in SAMSON come in. These tools let you create linear, circular, and curved patterns from atomic or molecular structures in just a few steps. Let’s take a closer look at how they work and how they can accelerate your workflow.
What Pattern Editors Do
Pattern Editors allow users to replicate selected molecular fragments and arrange them in well-defined patterns. This is particularly helpful for building:
- Carbon nanotubes
- Molecular wires and chains
- Cyclic nanostructures
- Curved or helical assemblies
SAMSON offers three types of pattern editors:
- Linear Pattern Editor – shortcut: L
- Circular Pattern Editor – shortcut: W
- Curved Pattern Editor – shortcut: Q
Each editor provides an interactive on-screen widget that lets you position, rotate, and replicate structures in real-time. Pattern generation is live and visually guided.
Creating a Carbon Nanotube (CNT) Manually
Here’s a practical example that illustrates how to use the editors: building a simple carbon nanotube manually.
- Create a ring of carbon atoms. Remove any hydrogens and align the ring using orientation tools.
- Activate the Circular Pattern Editor (W) to duplicate the ring:
- Set the number of repetitions (e.g., 12 to make a circle)
- Adjust the radius to close the shape
- Accept the result to generate the fused ring
- Align the ring structure to the XY plane using Edit > Align.
- Use the Linear Pattern Editor (L) to duplicate the ring stack along the Z-axis for the tube:
- Define translation distance (e.g., 2 Å)
- Optional: apply incremental rotation for helicity
- Minimize the structure to optimize geometry and optionally add hydrogen atoms.
This results in a manually created carbon nanotube made of precisely aligned rings stacked along an axis. Thanks to the pattern editors, such a task can now be completed in minutes rather than hours.
Precision Controls and Preferences
The editors support mouse-based manipulation for fast placement and also offer fine-tuned control:
- Ctrl or Cmd + Click to enter numeric values
- Mouse wheel to adjust the number of copies
- Snapping to control spacing and angles
You can also go into Preferences > Edit > Create pattern to:
- Auto-merge atoms within bonding distances
- Decide whether to add hydrogen atoms
- Choose to group or merge new elements with existing ones
Learn More
For more detailed instructions, video demonstrations, and feature descriptions, visit the official SAMSON documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.