Building a long molecular structure one copy at a time is tedious—and small placement errors can accumulate. A better approach is to make a useful repeating unit, arrange copies with a pattern editor, and then refine the resulting geometry. In SAMSON, this workflow can be used to construct a carbon nanotube from a ring.
The key idea is to separate the job into two manageable operations: first make a ring that can close cleanly, then stack copies of that ring along an axis. Pattern editors duplicate and arrange selected structures; they do not remove the need to check alignment and minimize the final geometry.
1. Prepare the repeating unit
Create a ring, remove its hydrogen atoms, and rotate it so its edges are aligned as needed. This preparation matters because the circular pattern will repeat the structure you select. Taking a moment to orient the ring before duplication makes it easier to see whether adjacent copies are positioned as intended.
You can create or load a structure, then select the atoms or molecular structure to duplicate. The pattern editors are available from the Editors Toolbar or through the Find everything… bar. The shortcuts are W for Circular Pattern, L for Linear Pattern, and Q for Curved Pattern.
2. Close the ring with a circular pattern
Activate the Circular Pattern Editor and increase the number of instances—for example, to 12. Adjust the radius until the edges of neighboring copies line up. The on-screen widget gives live visual feedback, so use it to inspect the arrangement before accepting it.
For greater control, drag the widget handles or hold Ctrl on Windows/Linux or Cmd on macOS while clicking a widget to enter precise values. Snapping can help keep translations and rotations at consistent increments. When the copies are aligned, accept the pattern. The documented workflow uses the option to merge overlapping atoms, which can turn the arranged copies into a single ring.
3. Stack rings along an axis
Align the ring to a convenient plane, such as the XY plane, using Edit > Align. Then select the ring and activate the Linear Pattern Editor. Set the translation along the Z-axis; 2 Å is an example value from the workflow. If the geometry calls for it, set an incremental rotation between copies as well.
Adjust the number of copies with the mouse wheel while hovering over the central widget. Holding Ctrl or Cmd while scrolling changes the count more quickly. Before accepting, check the spacing and orientation down the length of the structure. Accepting finalizes the repeated arrangement.
4. Refine after construction
Once the tube has been assembled, minimize the geometry to relax it. Hydrogens can also be added if needed. This final step is important: arranging copies establishes the structure’s repeated shape, while minimization helps refine its geometry. You can also review the pattern preferences under Preferences > Edit > Create pattern (circular / curved / linear), including options for nearby-atom merging, hydrogen adjustment, and whether generated structures are grouped or combined.
SAMSON includes interactive tutorials for foundational tasks such as building with atoms.
This ring-then-stack strategy is useful whenever a larger structure can be built from a repeating unit. The same pattern editors also support linear, circular, and curved arrangements for other molecular modeling tasks. For the complete workflow and video tutorials, see the SAMSON guide to creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.