When modeling nanoscale systems, one recurring challenge is replicating molecular units along a specific direction with precision. Whether building DNA-inspired nanostructures, polymer chains, or carbon nanotubes, manually duplicating and aligning units is both time-consuming and error-prone.
The Linear Pattern Editor in SAMSON addresses this issue by offering an intuitive visual tool to replicate, transform, and position repeated molecular elements along a linear axis. Here’s how it works and how it might fit into your modeling workflow.
What is the Linear Pattern Editor?
The Linear Pattern Editor allows you to quickly generate copies of atoms, molecules, or substructures arranged in a straight line and aligned precisely along a selected axis. Once an atomic selection is made, the editor creates an interactive widget that lets you:
- Translate and rotate duplicated structures along the X, Y, or Z axis.
- Adjust spacing between copies using mouse interaction or numerical input.
- Vary the number of copies on the fly using your mouse scroll wheel.
When to Use It
This tool can assist in designing large, periodic systems such as:
- Polymeric chains in materials science
- Peptide repeats in biomolecular models
- CNTs and other nanotechnology-inspired linear structures
How to Use the Linear Pattern Editor
- Prepare the structure: Start by building a molecule or loading an existing one in SAMSON. Select the atoms or molecular fragment you want to duplicate.
- Activate the editor: Press the shortcut key L or find the editor in the Editors Toolbar.
- Adjust positioning: Use on-screen controls to set translation distance and rotation between duplicates. Click on the widget center to input precise values.
- Set number of copies: Scroll to increase or decrease the number of replicas, or hold Ctrl/Cmd while scrolling for larger changes. You’ll immediately see the resulting pattern update in real time.
- Finalize: Click the green checkmark to apply the changes and generate the full structure.
Visual Example
Here’s an image that shows an interactive tutorial for building with atoms, which you can combine with pattern-based modeling:
Advanced Options
You can refine how patterns are built by opening Preferences > Edit > Create pattern (linear). There, you can enable merging of nearby atoms, hydrogen adjustment, and control how the generated pattern interacts with existing structures (e.g., combining or grouping).
Final Notes
For further structure control, SAMSON also provides alignment and distribution tools to evenly space and organize molecules in 3D scenes.
To explore other pattern types, such as curved or circular arrangements, visit the documentation below.
📘 Learn more about pattern creation in SAMSON
SAMSON and all SAMSON Extensions are now free for non-commercial use. This allows researchers, students, and educators worldwide to access powerful molecular modeling tools without cost.