Building a nanotube from scratch can feel less like molecular design and more like a geometry puzzle: the ring must close, neighboring edges need to meet, and the repeating units must be spaced and oriented consistently. Pattern editors in SAMSON help turn that repetition into a controlled workflow. Instead of placing every copy by hand, you can create a ring from a selected structure, then extend it into a tube.
The key idea is to separate the task into two manageable steps: first make the circumference, then build along the tube’s axis. This is useful whenever a structure can be assembled from a repeated unit—and it makes adjustments easier to reason about. If the ring needs a different radius, you can address that before stacking copies into a longer structure.
1. Prepare a repeat unit
Start by creating a ring structure in SAMSON. The documented nanotube example uses a ring with hydrogen atoms removed, then rotates it so its edges are oriented appropriately for joining. If you need a refresher on creating or transforming structures, see the guides to building molecules and moving objects.
Before making copies, select the structure you intend to duplicate. Selection matters: the pattern editor works on the selected atoms or structures, so a quick check of what is highlighted can prevent an unintended pattern.
2. Close the circumference with a circular pattern
Activate the Circular Pattern Editor with the W shortcut, or find it through the Editors Toolbar or the Find everything… bar. Increase the number of instances—for example, the documentation’s sample workflow uses 12—and adjust the radius until the ring’s edges align as intended.
For finer control, drag the editor’s on-screen handles to position and rotate the copies. To enter precise translation or rotation values, hold Ctrl on Windows/Linux or Cmd on macOS while clicking a widget. Snapping can help keep repeated adjustments consistent. These controls are useful when visual placement alone is difficult to reproduce.
When the arrangement looks right, click Accept. The documented workflow uses this step to merge overlapping atoms into a single ring. You can also review pattern-related options under Preferences > Edit > Create pattern (circular / curved / linear), including whether nearby atoms are merged and whether generated structures are grouped or combined with existing ones.
3. Extend the ring into a tube
Align the completed ring—for example, to the XY plane—using Edit > Align. Then select the ring and activate the Linear Pattern Editor with the L shortcut. Set the translation along the Z-axis; 2 Å is the example spacing given in the documentation. If the repeating units need a twist to match their edges, adjust the incremental rotation between copies.
As with the circular pattern, use the widget for interactive placement or enter values precisely with the Ctrl/Cmd-click method. To change the number of copies, scroll while hovering over the central widget; holding Ctrl or Cmd while scrolling changes the count more quickly. Review the preview before accepting, then click Accept to create the extended structure.
4. Check and relax the result
Patterning establishes a repeated arrangement; it does not replace checking the resulting geometry. Inspect the joins and overall shape, then use SAMSON’s minimization workflow to relax the geometry. The documentation also notes that hydrogens can optionally be added. If atom merging or hydrogen adjustment is relevant to your setup, check the pattern preferences before repeating the operation.
This ring-then-stack approach makes a large construction easier to troubleshoot: if the tube does not look right, you can revisit the ring’s instance count and radius separately from the linear spacing and rotation. It is a practical way to build repeated nanoscale structures without manually positioning every unit.
For the full editor overview and additional examples, learn more in the SAMSON documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.