One common frustration among molecular modelers is the time-consuming process of creating repetitive molecular structures, whether you’re stacking rings for a nanotube, arranging proteins in symmetric assemblies, or generating repeating motifs in nanomaterials. Precise alignment, duplication, and spatial control over a large number of atoms can quickly become tedious, even error-prone, without the right tools.
If you’ve found yourself manually copying molecules and repositioning them one by one, SAMSON’s Pattern Editors might offer a major improvement to your workflow. These tools are designed to help you replicate molecular structures in linear, circular, and curved arrangements in just a few interactive steps—ideal for generating complex architectures from simple building blocks.
What Are Pattern Editors?
SAMSON offers three Pattern Editors:
- Linear Pattern Editor: duplicates structures along a straight line (shortcut: L)
- Circular Pattern Editor: arranges structures in a circular loop (shortcut: W)
- Curved Pattern Editor: builds structures along user-defined curves (shortcut: Q)
Each editor provides live feedback while positioning and rotating copies of your selected atoms or molecules. You can interactively drag handles or enter precise transformations. The result? You can go from a single molecule to a complex patterned system in less than a minute.
When Should You Use Pattern Editors?
These tools are especially useful when creating structures like:
- Carbon nanotubes or nanorings
- Helical and circular biomolecular complexes
- Layered or tiled crystalline materials
You can use them to build structures atom-by-atom or apply them after importing molecular fragments.
Step-by-Step: Creating a Carbon Nanotube
Let’s walk through how you’d manually create a carbon nanotube using Pattern Editors:
- Build a carbon ring: Use the molecule-building tools to create a cyclic structure. Remove hydrogen atoms and rotate for edge alignment.
- Use the Circular Pattern Editor (W):
- Increase the number of copies (e.g., 12) until a complete ring forms.
- Adjust the radius to ensure carbon atoms are in bonding distance.
- Click ‘Accept’ to finalize and merge overlapping atoms.
- Align the ring to the XY plane using
Edit > Align. - Stack the rings with the Linear Pattern Editor (L):
- Translate along the Z-axis (e.g., 2 Å) to form a tube.
- Optionally, rotate each copy for a chiral nanotube.
- Accept the pattern to complete the structure.
- Minimize the resulting structure to relax atomic positions.
Fine-Tune Your Patterns
Within Preferences > Edit, you can further customize how patterns behave:
- Automatically merge atoms that are close together
- Adjust hydrogen atom handling
- Decide whether to group or combine the new structure into existing ones
Additionally, Edit > Align / Distribute offers ways to align or evenly distribute components, helping you maintain symmetry and order in large assemblies.
Interactive Control
Pattern Editors come with intuitive widgets. You can:
- Scroll the mouse to increase/decrease copies
- Use modifier keys (e.g., Ctrl or Cmd) for precision settings
- Snap transformations to chosen increments
This combination of manual and assisted control makes it fast to try different configurations and settle on the most chemically meaningful one.
Need a Visual Example?
The image below shows how one of SAMSON’s interactive tutorials can help you get started with atoms and pattern creation:
With a few clicks, thousands of atoms can be arranged into detailed nanostructures, with perfectly controlled geometry and symmetry. This reduces hours of setup into minutes of visual editing.
Learn more and explore pattern creation tools at SAMSON’s official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.