Designing carbon nanotubes or other tube-like molecular structures has traditionally required a combination of scripting skills, structural chemistry knowledge, and often repetitive modeling steps. If you’re working in nanotechnology, materials science, or molecular modeling, you’ve likely spent time trying to align rings just right—only to end up frustrated with small mismatches that become tedious to resolve.
With the Pattern Editors in the SAMSON platform, there’s now a user-friendly alternative that doesn’t require any coding or dry graphical alignment work. You can create carbon nanotube structures from scratch using visual tools. This blog post walks through how to build a nanotube by combining circular and linear patterns.
Why patterns make sense
Carbon nanotubes are essentially arrays of repeating units—commonly rings—stacked along an axis. Since this repetition is regular, it lends itself especially well to copy-transform workflows. Leveraging SAMSON’s Pattern Editors allows you to build structures like these in a few intuitive steps with visual fine-tuning where necessary.
Step-by-step: Manual Construction of a Nanotube
- Create a basic ring of atoms (e.g., benzene or a hexagonal carbon ring). Then remove hydrogen atoms to leave open ends for bonding.
- Rotate or align the ring as needed using the viewport controls or the
Edit > Aligntools to position its plane correctly. - Activate the Circular Pattern Editor by pressing
W. Increase the number of replicas (e.g., 12) and adjust the radius until the atoms align to form a ring-shaped nanostructure. Overlapping atoms fuse into single bonds once you Accept the pattern. - Align the result to the XY plane. The Align tool in the GUI lets you achieve this precisely via compass or axis alignment options.
- Use the Linear Pattern Editor (shortcut
L) on the completed ring. Set the translation along the Z-axis (e.g., 2 Å increments), and replicate copies to stack rings into a tube. You can also apply a small rotational offset to each layer, depending on the symmetry you want. - Finalize the structure by clicking Accept. For chemical realism, you may optionally minimize the structure and re-add hydrogens using SAMSON’s molecules and minimization tools.
Interactive control with minimal setup
Each Pattern Editor provides on-screen widgets that let you control placement, rotation, and repetition amounts with drag handles or precise input boxes. If you hold Ctrl (Windows/Linux) or Cmd (macOS), you can type in exact values for spacing or angles. There’s also smart snapping to control resolution for translations and rotations.
This gives you real-time feedback when adjusting geometry, which is especially helpful when dealing with cylindrical assemblies where symmetry is visually apparent.
Preview from the tutorial
Who might find this useful?
This workflow is particularly practical for molecular modelers working on nanostructure design, quick prototyping of helical assemblies, or those teaching molecular geometry where visual construction methods help clarify concepts. Because the method is fully visual, it can be a good introductory step before switching to scripting workflows for more automation.
To learn more about pattern-based molecular design in SAMSON, visit the full documentation at https://documentation.samson-connect.net/users/latest/creating-patterns/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.