Building a nanotube from individual atoms can become a repetitive exercise in copying, rotating, and checking alignment. The challenge is not just making a tube-shaped arrangement: the repeated units need to meet in a useful way, and the geometry may need refinement afterward. In SAMSON, circular and linear pattern editors can turn that sequence into a manageable workflow: make a ring, arrange copies around a circle, then stack rings along an axis.
This approach is useful when you want to construct a simple carbon nanotube manually and understand how its larger structure is assembled from repeated units. The values below are examples, not universal settings; the right number of copies, radius, and spacing depend on the ring and the structure you are building.
1. Prepare the building block
Start by creating a ring. Remove its hydrogen atoms, then rotate the ring so its edges are oriented appropriately for joining copies. This preparation matters: a pattern editor can replicate and position a structure, but the starting orientation still affects how the repeated units meet.
Before making many copies, inspect the ring’s orientation in the viewport. If you need to adjust it, use SAMSON’s object-moving tools; the Moving objects guide covers moving and aligning structures.
2. Close the ring with a circular pattern
Select the prepared ring and activate the Circular Pattern Editor with W. Increase the number of instances—for example, to 12—and adjust the radius until the edges of neighboring copies line up. The editor’s on-screen controls provide visual feedback as you position and transform the copies.
When the arrangement looks right, accept it. If the pattern settings are configured to merge nearby atoms, overlapping atoms can be combined into a single ring. This is a useful point to check the result before continuing: the next step will repeat the completed ring many times, so correcting its arrangement now can save time later.
3. Stack rings into a tube
Align the completed ring—for example, with the XY plane—using Edit > Align. Then select it and activate the Linear Pattern Editor with L. Set the translation along the Z-axis; 2 Å is an example from the workflow, not a value to apply automatically. If needed, add an incremental rotation between copies to help match bonds.
To enter exact translation or rotation values, hold Ctrl on Windows or Linux, or Cmd on macOS, and click the relevant widget. You can also control translation and rotation snapping in the editor. To change the number of copies, scroll while hovering over the central widget; holding Ctrl or Cmd while scrolling changes the copy count more quickly. Accept the pattern when the tube has the desired length.
4. Refine the result
Pattern construction establishes the repeated arrangement; it does not replace checking or refining the resulting geometry. After building the tube, minimize it to relax the geometry, and add hydrogens if appropriate for your model. Preferences under Preferences > Edit > Create pattern (circular / curved / linear) let you control options such as merging nearby atoms, adjusting hydrogen atoms, and grouping or combining generated structures.
The same editors are useful beyond nanotubes whenever a model contains a repeated unit: the circular editor arranges copies around a center, while the linear editor repeats them along a direction. For translations and rotations that need to be exact, use the numerical widget controls rather than relying only on visual placement.
For the complete instructions and related pattern-editor details, visit the SAMSON guide to creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.