Building a nanotube from repeated molecular units can become tedious quickly. Placing each copy by hand makes it harder to keep spacing and orientation consistent—and small placement errors can accumulate along the structure. A more controlled approach is to build a ring first, then use pattern editors to repeat that ring along an axis.
This workflow uses SAMSON’s Circular and Linear Pattern editors. The example values below, such as 12 ring instances and 2 Å spacing, are starting points from the documentation, not universal settings. The right geometry depends on the structure you are assembling.
1. Prepare a clean repeating unit
Create a ring in SAMSON, remove its hydrogen atoms, and rotate it so the edges you intend to connect are aligned. This preparation matters: a pattern editor can repeat a structure precisely, but it cannot correct an unsuitable orientation in the starting unit.
Before making copies, check that the ring is selected. Pattern editors duplicate the selected structure, so an incorrect selection can produce a pattern of the wrong object. If you need a refresher on selection or building, see the Selecting and Building molecules guides.
2. Close the ring with the Circular Pattern editor
Activate the Circular Pattern editor from the Editors Toolbar or the Find everything… bar. Its shortcut is W. Increase the number of instances—for example, to 12—and adjust the radius until neighboring edges line up as intended.
Use the on-screen widget 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 make repeated adjustments more regular. The mouse wheel over the central widget changes the number of copies; holding Ctrl or Cmd while scrolling changes the count more quickly.
Inspect the preview before accepting it. In particular, check the ring’s closure and the alignment of the edges that should meet. When the arrangement looks right, click Accept. The documentation notes that overlapping atoms can be merged into a single ring; related behavior can be adjusted under Preferences > Edit > Create pattern (circular / curved / linear).
3. Align the ring, then extend it
Once the ring is formed, align it—for example, to the XY plane—using Edit > Align. This gives you a clear reference for the direction in which to build the tube.
Select the ring and activate the Linear Pattern editor with L. Set the copies to translate along the Z-axis. The documented example uses 2 Å as a starting spacing; adjust this to suit the structure and the intended connections. If needed, set an incremental rotation between copies as well. You can enter precise values through the widget rather than relying only on dragging.
Preview the stack and check that the rings remain consistently spaced and oriented. Accept the pattern to create the extended structure. The Curved Pattern editor, shortcut Q, is another option when the desired arrangement follows a curve rather than a straight axis.
4. Review and refine the result
After patterning, minimize the structure to relax its geometry, and add hydrogens if appropriate for your next modeling step. Pattern preferences also let you choose whether generated structures are grouped or combined with existing ones, and whether nearby atoms are merged automatically. These choices affect how the result is organized, so it is useful to check them before creating a large pattern.
The key idea is to separate the task into two manageable operations: first make a well-aligned repeating ring, then replicate that ring along a chosen direction. This is easier to inspect and adjust than positioning every unit individually, and the pattern widgets allow both interactive placement and precise numerical control.
For the original instructions and video tutorial, see Creating patterns in SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.