One common challenge in molecular modeling — especially in nanotechnology, materials science, or biophysics — is replicating complex structural motifs across different geometrical arrangements. Whether you’re trying to build a carbon nanotube, create a crystalline structure, or arrange proteins in a symmetric fashion, duplicating and aligning molecules manually can quickly become inefficient.
This is where SAMSON’s Pattern Editors can help. They allow you to create linear, circular, or curved patterns of selected molecular fragments or entire structures in just a few steps.
Why use pattern editors?
Pattern Editors are designed to:
- Accelerate the construction of large and repetitive molecular systems
- Maintain precision with atomic-level transformations
- Provide visual feedback for each edit
Whether you’re building polymer chains, modeling nanotubes, or designing nanomaterials, pattern editors simplify and speed up your workflow — all without any scripting or manual duplication.
How it works
Let’s say you’ve created or imported a molecular motif — this might be a benzene ring, a protein fragment, or a custom input structure. Here’s how you can quickly duplicate and arrange it using SAMSON’s Pattern Editors:
- Select the structure you want to replicate (atoms, groups, or entire molecules).
- Activate a Pattern Editor:
- Linear Pattern: Press
L - Circular Pattern: Press
W - Curved Pattern: Press
Q - Use the on-screen widget to position/rotate each replica:
- Drag handles interactively to adjust placement
- Hold
Ctrl/Cmdfor precise inputs (e.g., 2 Å spacing) - Enable snapping for consistent rotation/translation
- Set the number of copies directly by scrolling over the central widget:
- Scroll your mouse wheel
- Hold
Ctrl/Cmd+ scroll to change faster
- Press Accept to finalize the generated pattern.
Example: Linear Pattern Replication
Start with a small molecule, like a methane or a functional group you wish to repeat. Once selected, activate the Linear Pattern Editor. From here:
- Adjust the translation vector (X, Y, or Z direction)
- Set the number of instances
- Preview changes instantly through live feedback
For more complex manipulations, you can go into Preferences > Edit and control whether to automatically merge nearby atoms, adjust hydrogens, or group resulting structures.
Build Nanotubes Manually
Another great use case is constructing custom carbon nanotubes. You can manually create a ring, use the Circular Pattern Editor to close it, and then stack them using the Linear Pattern Editor. This gives full control over the geometry and bonding of each element.
Interactive Controls
All pattern editors in SAMSON provide interactable 3D widgets that allow quick pattern setup — great for those who prefer visual modeling and minimal typing. They are especially helpful when you need to make quick iterative changes and visually inspect the outcome before committing to the final structure.
Where to find these tools
The Pattern Editors are available under the Editors Toolbar on the left of your viewport, or you can search for them using the “Find everything…” bar at the top of the SAMSON interface.
This functionality is part of the reason SAMSON is used across disciplines from biomolecular modeling to advanced nanofabrication. It reduces repetitive effort and frees up time for scientific creativity.
To learn more and explore interactive examples, visit the full documentation page:
https://documentation.samson-connect.net/users/latest/creating-patterns/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.