Building a repeated molecular structure one copy at a time is tedious—and it is easy to lose consistent spacing or alignment along the way. For structures such as a nanotube, the challenge is not only making many copies: the pieces must also be arranged so their edges can meet as intended. SAMSON’s pattern editors let you build repetitions interactively, then refine the arrangement with precise values.
The key is to treat the task as two smaller operations: first make a circular ring from a selected building block, then extend that ring along an axis. This separates the circular arrangement from the linear repetition and makes it easier to inspect each stage before proceeding.
Start with a suitable building block
Create or load the structure you want to repeat, then select it before activating a pattern editor. For the nanotube workflow, the documentation uses a ring: create one, remove hydrogen atoms, and rotate it to align its edges. Those preparation steps matter because the pattern tool duplicates the selected structure; it does not decide how the building block should be oriented for you.
If you are new to SAMSON’s document and viewport controls, this screenshot accompanies one of the interactive tutorials on building with atoms:
Make the circular section first
With the ring selected, activate the Circular Pattern Editor using W. Increase the instance count—for example, to 12—and adjust the radius until neighboring edges line up as desired. The on-screen widget provides live visual feedback as you position and rotate the copies.
For more controlled adjustments, hold Ctrl on Windows or Linux, or Cmd on macOS, while clicking a widget to enter precise translation or rotation values. Snapping can also help keep movements and angles consistent. When the circular arrangement looks right, accept it. With the relevant preference enabled, nearby atoms can be merged; the documented nanotube example uses this to join overlapping atoms into a single ring.
Extend the ring into a tube
Next, align the completed ring—for example, to the XY plane—using Edit > Align. Select the ring and activate the Linear Pattern Editor with L. Set the translation along the Z-axis; 2 Å is an example given in the documentation, not a universal spacing value. If needed, set an incremental rotation between replicas to help match bonds.
Adjust the number of copies by scrolling over the central widget. Holding Ctrl or Cmd while scrolling changes the count more quickly. Before accepting, check the spacing, orientation, and visible alignment of the repeated rings. Then accept the pattern to create the extended structure.
A few checks that save time
- Confirm the selection. Pattern editors duplicate the selected structure, so check that the intended ring or molecule is selected before starting.
- Separate arrangement from repetition. Build and inspect the circular section before stacking it linearly.
- Use exact values when alignment matters. Dragging is useful for exploration; precise widget values and snapping help make adjustments repeatable.
- Review pattern preferences. In Preferences > Edit > Create pattern (circular / curved / linear), you can choose whether to merge nearby atoms, adjust hydrogen atoms, and group or combine generated structures.
- Relax the result. The documented workflow recommends minimizing the structure after patterning and optionally adding hydrogens.
The same editors support other repeated arrangements too: the Linear Pattern Editor uses L, the Circular Pattern Editor uses W, and the Curved Pattern Editor uses Q. Each offers a way to position, rotate, and duplicate selected structures with interactive controls.
For the complete walkthrough and additional pattern-building guidance, see the SAMSON documentation on creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.