Building a nanotube from atoms can become tedious when every repeated unit has to be positioned by hand. Small differences in spacing or orientation can also make it harder to line up neighboring parts. A practical way to reduce that manual work is to build the structure in stages: make a ring, arrange copies around a circle, then repeat the completed ring along an axis.
This workflow uses SAMSON’s Circular and Linear Pattern Editors. It is useful not only for nanotubes, but also whenever a molecular model contains a repeated unit arranged along a circular path and then extended in one direction.
1. Prepare a repeat unit
Start by creating or loading the structure you want to repeat. For the nanotube example, the documentation uses a ring. Remove hydrogen atoms and rotate the ring so its edges are oriented as needed for connecting neighboring copies. Select the structure before activating a pattern editor; the selected atoms or structure are what the editor duplicates.
Take a moment to check the orientation before making copies. A pattern editor can replicate a structure, but it does not replace the modeling decisions about which parts should meet or how they should be aligned. If you need to reposition the ring, SAMSON provides move tools and alignment commands before you begin patterning.
2. Close the ring with the Circular Pattern Editor
Activate the Circular Pattern Editor with W. Use its on-screen widget to set the arrangement and increase the number of instances—for example, the documentation uses 12 copies to form a closed ring. Adjust the radius until the edges of neighboring copies align as intended.
The widget provides live visual feedback, so inspect the arrangement before accepting it. You can drag handles for interactive adjustments. For more precise translations or rotations, hold Ctrl on Windows or Linux, or Cmd on macOS, and click a widget to enter values. Snapping can help control translation distances and rotation angles.
When the ring looks right, click Accept. If nearby atoms should become part of one connected structure, check the pattern preferences for the option to automatically merge nearby atoms. This preference is especially relevant to the ring-building step; it is still worth inspecting the result rather than assuming the geometry is correct.
3. Align the ring, then extend it
Align the completed ring to a convenient plane, such as the XY plane, using Edit > Align. Establishing a clear orientation first makes the next operation easier to reason about: the Linear Pattern Editor can then extend the ring along the intended axis.
Select the ring and activate the Linear Pattern Editor with L. Set the translation along the Z-axis; 2 Å is an example value from the documentation, not a universal spacing for every structure. If the repeating units need a twist to match their edges, set an incremental rotation as well. The appropriate spacing and rotation depend on the structure you are modeling, so treat the widget values as parameters to inspect and adjust.
As with circular patterning, use the handles for quick changes or enter precise values through the widget. The mouse wheel over the central widget changes the number of copies; holding Ctrl or Cmd while scrolling changes the count more quickly. Review the preview, then click Accept to create the extended structure.
4. Check and refine the result
After the pattern is created, inspect the geometry and the contacts between repeated units. If the model needs further refinement, the documented workflow recommends minimizing the structure to relax its geometry and optionally adding hydrogens. Pattern construction establishes the repeated arrangement; minimization is a separate step for refining the resulting geometry.
For a more controlled workflow, adjust one variable at a time: first the ring radius, then the ring’s orientation, then the linear spacing or rotation. This makes it easier to identify which setting needs attention if the copies do not meet as expected. Preferences under Preferences > Edit > Create pattern (circular / curved / linear) also let you choose whether generated structures are grouped or combined with existing ones, and whether hydrogens are adjusted.
The key idea is to treat a large repeated structure as a sequence of manageable modeling tasks: prepare a suitable unit, arrange it into a ring, orient the ring, and extend it. SAMSON also includes a Carbon Nanotube Editor, accessible from the Editors Toolbar or the Find everything bar. To explore the pattern editors and their controls in more detail, see the original documentation on creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.