Designing large molecular systems is often a time-consuming process. Whether you’re working in nanotechnology, material science, or biomolecular modeling, repeating structural units into larger assemblies—like polymer chains, rings, sheets, or nanotubes—typically requires manual duplication, alignment, and estimation. This step alone can eat up hours of valuable development time.
But what if building an extended molecular structure was as simple as selecting, duplicating and rotating, all with visual feedback in real time?
This is exactly what SAMSON’s Pattern Builders are designed to help with. SAMSON includes three editors that make it significantly easier to replicate and arrange molecular fragments:
- Linear Pattern Editor (L)
- Circular Pattern Editor (W)
- Curved Pattern Editor (Q)
Instead of manually building repetitive patterns, you can select a structure — such as a ring, small molecule or atomic cluster — and duplicate it in seconds. Each editor comes with a widget in the viewport to precisely position, rotate, and copy your selection.
Common Pain: Building Structures That Repeat
Many molecular modelers spend time creating structures like carbon nanotubes, ligand arrays, or biomolecular chains. The process often involves repeating subunits and manually adjusting distances, sometimes in 3D space where exact placement gets tricky.
The Pattern Builders address this by providing interactive tools with visual feedback, snapping functionality, and input fields for exact values. For example, to create a nanotube:
- You can create a carbon ring, rotate it, and arrange it into a larger ring using the Circular Pattern Editor.
- Once the ring is formed, the Linear Pattern Builder can be used to stack rings along the Z-axis, forming a tube.
- With settings like spacing (e.g., 2 Å) or incremental rotational adjustments per ring, precise and complex structures become easy to build.
Because overlapping atoms are automatically merged and hydrogen atoms can be adjusted after the patterns are finalized, the result is chemically realistic and ready for optimization (e.g., minimization).
Interactive and Visual
Pattern Builders let you build large arrays or complex geometries with live previews. Want 30 copies of a molecule along a curve? Hold Ctrl (or Cmd on macOS), click a widget, and enter exact coordinates or rotation angles. You can also scroll the mouse wheel to increase the number of copies, and see changes instantly in 3D.
The editors are accessible from the Editors Toolbar or the Find everything… search bar. When you’re satisfied with the result, clicking the checkmark finalizes the pattern.
Advanced Settings
Preferences allow you to customize how newly-created structures interact with existing ones. For example, you can:
- Automatically merge nearby atoms.
- Adjust hydrogen atoms post-duplication.
- Group or combine new structures with existing ones.
You can also align or distribute structural components after patterning using SAMSON’s alignment tools, which is ideal for creating organized arrays or optimizing geometry before simulation.
Where to Learn More
This feature is particularly useful when building nanotubes, sheets, or any repeated molecular motif. If you want a quick demonstration, there’s a tutorial extract available from the 2025 SAMSON webinar and interactive tutorials you can follow right in SAMSON.
To explore Pattern Builders in more detail, visit the full documentation at https://documentation.samson-connect.net/users/latest/creating-patterns/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started with SAMSON at https://www.samson-connect.net.