Creating repetitive molecular structures—such as polymers, nanotubes, or crystal lattices—can be one of the more time-consuming and error-prone tasks in molecular modeling. When you need to replicate molecular fragments with precise positioning, structure builders often find themselves tediously copying, pasting, rotating, and aligning over and over. Mistakes add up, and the joy of design quickly turns into repetitive strain.
That’s where SAMSON’s Pattern Editors come in. These integrated tools let you repeatedly replicate molecular fragments in linear, circular, or curved patterns, with real-time visual feedback and precise control—right inside your molecular design session.
Why Pattern Editors Can Help
Imagine you’ve built a five-atom monomer and want to assemble a chain of 100 such molecules, maintaining exact relative orientation and bonding distance. Or maybe you want to create a circular DNA nanoring or wrap molecules around a carbon nanostructure. Instead of manual duplication and adjustment, use a Pattern Editor that includes widgets to position, rotate, and replicate with a few clicks.
Three Included Pattern Editors
- Linear Pattern Editor: Use this to extend structures along a straight direction (shortcut: L).
- Circular Pattern Editor: Replicate around a central axis (shortcut: W).
- Curved Pattern Editor: For arcs or custom bends (shortcut: Q).
Each editor lets you control the arrangement using drag handles and numerical input for translations and rotations, and set snap steps for alignment. Once you’re satisfied with the configuration, click Accept to generate the final structure.
Useful Shortcuts and Tips
Here are some ways to make the most of Pattern Editors:
- For fine adjustments, hold Ctrl (Windows/Linux) or Cmd (macOS) and click the widget center to input exact values.
- Scroll your mouse while hovering over the duplication widget to adjust the number of instances quickly.
- Enable snapping to ensure consistent spacing between replicated units.
Want to stack a ring into a carbon nanotube? Duplicate it linearly along an axis. Want to create a protein groove or nanoring? Use the circular pattern editor. You can even switch editors midway if needed for combining conformations.
Example: Visual Duplication with the Linear Pattern Editor
- Create or load a molecule and select the atoms you’d like to replicate.
- Activate the Linear Pattern Editor by pressing L.
- Use the widget to set desired spacing and rotation between copies.
- Click the center of the widget to enter precise alignment values (for example, 2 Å translations along Z).
- Scroll to set replication count, then click Accept.
This method not only saves time but reduces the risk of misalignment and helps with consistency when preparing structures for simulation or visualization.
Ready to Try It?
To see detailed steps, example workflows, and video demonstrations, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.