Building a nanotube from scratch can feel like a small task repeated far too many times: place a ring, position another one, check the spacing, and repeat. The hard part is not just making copies. The rings must be oriented and spaced consistently, and their edges need to meet as intended. In SAMSON, circular and linear pattern editors let you build this structure in two stages: first make a ring, then extend it into a tube.
This workflow is useful when you want direct control over how a repeated structure is assembled. The values below—such as 12 ring instances and a 2 Å translation—are examples from the guide, not universal settings for every model.
1. Prepare the unit you want to repeat
Start by creating a ring, then remove its hydrogen atoms and rotate it so the edges are aligned for the next construction step. This preparation matters: a pattern editor duplicates the structure you select, so the orientation of that starting unit carries through to every copy.
If you are new to building or orienting structures in SAMSON, the interactive tutorial image below is a useful starting point for getting familiar with the viewport and basic building operations.
2. Close the ring with a circular pattern
Select the prepared ring and activate the Circular Pattern Editor with W, or find it in the Editors Toolbar or the Find everything… bar. Increase the number of instances—for example, to 12—and adjust the radius until the edges line up for bonding.
Use the live preview to inspect the arrangement before accepting it. When the ring looks right, accept the pattern. If the relevant preference is enabled, nearby atoms can be merged automatically; check Preferences > Edit > Create pattern (circular / curved / linear) to review that behavior. This is a useful point to verify the ring before building a longer structure: a spacing or orientation issue repeated around the ring will be harder to diagnose later.
3. Extend the ring along an axis
Align the completed ring—for example, to the XY plane—using Edit > Align. Then select it and activate the Linear Pattern Editor with L. Translate the copies along the Z-axis; 2 Å is an example starting value in the documented workflow. If the geometry calls for it, set an incremental rotation between copies so the repeated units meet as intended.
Pattern controls support both interactive placement and precise adjustments. Drag the widget handles to change the arrangement. For numeric translation or rotation values, hold Ctrl on Windows or Linux, or Cmd on macOS, and click a widget. Snapping can help keep changes to consistent distances or angles. To change the number of copies, scroll while hovering over the central widget; holding Ctrl or Cmd while scrolling changes the count more quickly. Inspect the preview, then accept to create the extended structure.
4. Check, then relax the geometry
Before moving on, inspect the assembled tube for obvious misalignment or unexpected spacing. Patterning makes repetition efficient, but it does not remove the need to check whether the chosen starting geometry, radius, spacing, and rotation suit your structure. Once the arrangement is ready, minimize it to relax the geometry. You can also add hydrogens if needed.
A short checklist
- Prepare and orient the ring before duplicating it.
- Check the circular pattern’s radius and instance count before accepting.
- Align the ring before stacking it linearly.
- Treat example distances as starting points, not fixed rules.
- Inspect the assembled structure and minimize it afterward.
This two-stage approach—circular repetition followed by linear repetition—turns a repetitive placement task into a sequence of geometry decisions you can preview and adjust. For editor details and related controls, see the SAMSON guide to creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.