If you’ve ever tried to build repetitive molecular structures manually — nanotubes, rings, or arrays — you know how tedious it can be to duplicate, rotate, and align atoms correctly. This is especially painful when working at the nanoscale level where errors are easy to miss, and even small misalignments can derail your model.
Thankfully, SAMSON provides dedicated Pattern Editors to take care of this task efficiently: the Linear Pattern Editor, the Circular Pattern Editor, and the Curved Pattern Editor. These tools can duplicate molecular units and arrange them precisely using interactive widgets, all in just a few clicks.
Why Pattern Editors Matter
Whether you’re modeling carbon nanotubes, simulating self-assembled biomolecular structures, or simply creating clean training data for your machine learning models, pattern creation is common — and time-consuming. Doing this manually introduces risk and slows your workflow.
With SAMSON’s Pattern Editors, you get a visual, interactive interface that lets you:
- Select a part of a molecular structure (atoms, rings, or whole molecules).
- Replicate it with linear, circular, or curved arrangements.
- Tweak translations, rotations, and snap settings interactively or via precise inputs.
- Visualize the final structure before committing.
Getting Started: A Carbon Nanotube Example
Let’s say you want to model a carbon nanotube. While SAMSON has a dedicated Carbon Nanotube Editor, you can construct one manually too – useful if you want more control over the design process:
- Create a small carbon ring (e.g., a 6-membered ring) and remove hydrogens.
- Align the ring properly using the rotation tools to match edges for bonding.
- Activate the Circular Pattern Editor (W) and increase the number of copies (e.g., 12) to complete a circular ring.
- Adjust the radius to align bonds and accept the result to finalize the ring.
- Align the full ring to a standard plane using Edit > Align.
- Use the Linear Pattern Editor (L) to stack multiple rings along the Z-axis — carefully tuning the spacing and (if needed) applying rotation to match bond orientations.
- Accept the pattern to finalize your nanotube architecture.
- Optionally, minimize the structure and add hydrogens.
Interactive Controls You Might Miss
Double-click the widget’s center to enter precise transformation values. Want to copy a unit every 2.5 Å along the Z-axis with exactly 30° rotation between them? No problem. For snapping behavior, you can fine-tune translation and rotation increments in the settings for more control.
Prefer a Guided Approach?
SAMSON includes tutorials like “Building with atoms” and “Moving objects in the Viewport” to help you get used to editor behavior. Here’s what the interactive tutorial interface looks like:
Final Touches and Preferences
Pattern duplication settings can be customized under Edit > Preferences to merge atoms that are close together, add hydrogens automatically, or control how duplicated molecules are grouped. Complement these with the alignment and distribution tools to ensure clean symmetry across your design.
To access the Pattern Editors at any time, click on the Editors Toolbar at the left of the viewport or use the Find everything… bar at the top of SAMSON’s interface.
From speeding up nanostructure creation to ensuring geometric reliability in your simulations, Pattern Editors help reduce repetitive actions and cut down human errors.
Learn more in the full SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.