Building a long molecular structure by placing every unit one at a time is tedious—and small alignment errors can accumulate as the structure grows. A more manageable approach is to make one repeat unit, arrange copies with pattern editors, then check and refine the result. In SAMSON, that workflow can be used to construct a carbon nanotube from a ring.
The key idea is to separate the task into two transformations: first arrange rings around a circle, then duplicate that ring along an axis. Before starting, make sure the source structure is oriented as intended and that you know which atoms should meet at the joins. Pattern editors duplicate the structure you select, so choosing the right unit is an important first step.
1. Prepare the repeat unit
Create a ring, remove its hydrogen atoms, and rotate it so its edges are aligned for joining. These preparation steps matter: the circular pattern will reproduce the ring’s current orientation, and the linear pattern will reproduce the circular structure you create. If the starting unit is misaligned, duplication will repeat that misalignment.
For help with these basics, SAMSON includes interactive tutorials on building with atoms and moving objects. The image below shows the interactive tutorial interface.
2. Close the ring with circular patterning
Select the prepared ring and activate the Circular Pattern Editor with W. Increase the instance count—for example, to 12—and adjust the radius until neighboring edges line up as intended. The editor provides an interactive widget with visual feedback, so you can inspect the arrangement before accepting it.
When the geometry looks right, accept the pattern. The documentation describes merging overlapping atoms into a single ring at this stage. You can also review Preferences > Edit > Create pattern (circular / curved / linear) for options such as automatically merging nearby atoms and choosing how generated structures are grouped or combined.
3. Stack 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 L. Set the translation along the Z-axis; the guide gives 2 Å as an example. If the bonds require it, add an incremental rotation between successive copies.
To set exact translations or rotations, hold Ctrl on Windows/Linux or Cmd on macOS while clicking a widget. You can also adjust snapping to control translation distances and rotation angles. Change the number of copies by scrolling over the central widget; holding Ctrl or Cmd while scrolling changes the count more quickly. Review the preview before accepting the extended structure.
4. Check and refine
Once the tube has been assembled, minimize the structure to relax its geometry. You can optionally add hydrogens as part of the follow-up workflow. The pattern preferences also include an option to adjust hydrogen atoms. These are refinement steps, not substitutes for checking that the ring radius, spacing, and orientation produced the intended connections.
A useful way to troubleshoot is to revisit the construction in order: confirm the starting ring orientation, check the circular radius and instance count, then check the linear translation and any incremental rotation. Since each stage builds on the previous one, isolating the stage where the alignment changes is often easier than adjusting the finished tube as a whole.
This ring-then-stack method illustrates a broader benefit of pattern building: instead of manually placing many copies, you can define a repeat unit and control its arrangement. The same linear, circular, and curved editors can help assemble other repeated molecular structures, with interactive positioning and precise values available when needed.
For more details and a video walkthrough, see the SAMSON guide to creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.