Creating large or repetitive molecular structures manually can be a frustrating and time-consuming task, whether you’re building nanotubes, simulating repetition in crystals, or prototyping nanoscale machines. Many molecular modelers spend hours copying, rotating, and aligning fragments, often repeating the same actions for each instance. But what if you could replicate and arrange molecular structures in just a few clicks?
SAMSON offers a solution through its Pattern Editors, a set of powerful tools designed to automate the replication of molecular units in linear, circular, or curved configurations. These editors can dramatically reduce repetitive editing, while offering intuitive, precise control.
What Are Pattern Editors?
SAMSON features three dedicated Pattern Editors, each corresponding to a specific type of replication geometry:
- Linear Pattern Editor – Use shortcut L
- Circular Pattern Editor – Use shortcut W
- Curved Pattern Editor – Use shortcut Q
You can access them from the Editors Toolbar on the left side of the viewport, or by typing their name in the “Find everything…” search bar.
How They Help
The pain point these editors address is clear: quickly building and modifying large, repetitive molecular structures. Whether you’re modeling DNA helices, replicating molecular fragments, or creating nanoscale simulations, pattern editors let you:
- Duplicate atoms, molecules, or fragments instantly in your chosen pattern
- Position and rotate replicas using interactive 3D widgets
- Adjust copy number with your mouse wheel in real-time
- Snap movements to precise rotation angles or translation distances
This means you no longer need to duplicate, rotate, and align structures manually, and you can modify your setup interactively before finalizing it with a single click.
Example: Creating a Linear Molecular Array
Suppose you’ve created a small molecule and want to extend it along a single axis to form a fiber-like structure:
- Select the initial molecule.
- Activate the Linear Pattern Editor (L).
- Drag the on-screen handles to adjust spacing and rotation.
- Use your mouse scroll wheel near the widget’s center to set the number of replicas.
- Click Accept to finalize the resulting array.
You can even hold Ctrl (or Cmd on macOS) and click a widget to enter precise values for translations and rotations. Snapping options let you lock transformations to specific increments.
Advanced Controls
SAMSON goes one step further by offering advanced preferences under Edit > Preferences where you can set behavior for each pattern type, such as:
- Automatically merging nearby atoms
- Adjusting hydrogen atoms
- Merging new structures with existing ones or creating separate entities
Additionally, the Pattern Editors work seamlessly with the Align and Distribute tools for post-pattern layout adjustments. This is ideal when building more complex, hierarchical systems.
Useful Across Disciplines
Pattern creation in SAMSON lends itself well to:
- Nanotechnology – design nanotubes, cages, or nanomachines
- Biomolecular modeling – generate polymers or ring structures
- Material science – model periodic crystals or repeating motifs
What used to take hours by hand can now be accomplished flexibly and precisely in seconds.
To learn more and watch video examples, visit the SAMSON documentation page on creating patterns.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.