Building a nanotube atom by atom is tedious—and repeating a structure without careful alignment can leave gaps or overlaps where units should meet. A more manageable approach is to build the tube in two stages: make a circular ring from a selected molecular unit, then repeat that ring along an axis. In SAMSON, the Circular and Linear Pattern Editors provide the duplication and positioning controls for this workflow.
The key is to treat each stage as a separate geometry problem. First, focus on how the units meet around the circumference. Then focus on the spacing and orientation of rings along the tube. Keeping those decisions separate makes it easier to adjust the pattern before accepting it.
1. Prepare the building block
Create a ring, remove its hydrogen atoms, and rotate it so the edges that should meet are aligned. This preparation matters: the pattern editor duplicates the selected structure, so it is worth checking the starting unit before making many copies. Select the structure you intend to duplicate.
2. Close the circumference
Activate the Circular Pattern Editor with W. Increase the number of instances until the copies form a closed ring; 12 is one example from the SAMSON workflow, not a universal setting. Adjust the radius so neighboring edges line up. Use the editor’s interactive widget to position the copies, and use its precise-value controls when you need a specific transformation. Snapping can help control translation distances and rotation angles.
Before accepting, inspect the arrangement: are the edges aligned, and does the ring close as intended? When the geometry is ready, accept the pattern. The documentation describes merging overlapping atoms into a single ring; pattern behavior can also be adjusted in Preferences > Edit > Create pattern (circular / curved / linear), including whether nearby atoms are merged. Check those preferences when the result does not match your intended construction.
3. Stack rings into a tube
Align the completed ring—for example, to the XY plane using Edit > Align. Select it, then activate the Linear Pattern Editor with L. Set the translation along the Z-axis; 2 Å is the example value in the guide, not a recommended spacing for every structure. If needed, add an incremental rotation between copies so the repeated rings match the intended bonding arrangement.
The editors let you adjust copy count by scrolling over the central widget. Hold Ctrl on Windows or Linux, or Cmd on macOS, while scrolling to change the count more quickly. For exact translations or rotations, hold the same modifier and click a widget to enter values. These controls help you tune spacing and orientation without relying only on dragging.
4. Finish and check the model
Accept the linear pattern to create the extended structure. Then minimize the geometry to relax it, and add hydrogens if needed. Treat the example distances and copy counts as starting points: the appropriate values depend on the structure you are building. If you need to reorganize structures, SAMSON also provides Edit > Align / Distribute.
This staged workflow is useful beyond nanotubes: whenever a model is built from repeated units, it helps to solve the local arrangement first and the larger-scale repetition second. See the SAMSON pattern-building documentation for more on linear, circular, and curved patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.