Building a long molecular structure by copying and positioning each part individually is tedious—and small alignment errors can accumulate. A carbon nanotube is a useful example: its repeating rings need to form a closed circumference, then stack along an axis. SAMSON’s Circular and Linear Pattern Editors let you construct that arrangement from a selected ring, while keeping spacing, rotation, and copy count adjustable before you commit.
The key idea: treat the tube as two patterning problems. First arrange a ring around a circle. Then use that completed ring as the unit to repeat along a line. This breaks a large construction task into two manageable steps.
1. Prepare a ring to repeat
Create a ring in SAMSON, remove its hydrogen atoms, and rotate it so its edges are oriented appropriately for joining. Select the structure you intend to duplicate before activating a pattern editor. Pattern editors act on the selection, so checking what is selected first helps avoid repeating unintended atoms or other structures.
The pattern editors are available from the Editors Toolbar or the Find everything… bar. The shortcuts are W for Circular Pattern, L for Linear Pattern, and Q for Curved Pattern.
2. Close the circumference
Activate the Circular Pattern Editor and adjust the number of instances and the radius. For example, 12 instances can form a closed ring; the exact radius matters because the edges need to meet in the intended arrangement. Use the on-screen widget to adjust the pattern and inspect the live preview rather than accepting the first placement.
When a widget needs a more exact value, hold Ctrl on Windows or Linux, or Cmd on macOS, and click it to enter a precise translation or rotation. Snapping can help control translation distances and angles. Once the ring looks correctly arranged, choose Accept. SAMSON’s pattern preferences include an option to merge nearby atoms, which is relevant when overlapping atoms should become a joined structure.
3. Turn 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. Set the repeated translation along the Z-axis; the documented example uses 2 Å. Adjust the incremental rotation between copies if needed to match the bonds, and inspect the preview as you change the settings. Accept when the stack has the intended spacing and orientation.
For either editor, the mouse wheel over the central widget changes the number of copies. Holding Ctrl or Cmd while scrolling changes the count more quickly. This makes it practical to refine copy count without rebuilding the pattern from scratch.
Before you finalize
- Check the selection: only the intended ring or structure should be repeated.
- Check geometry in stages: inspect the circular arrangement before using it as the unit for the linear pattern.
- Use precise values when alignment matters: widget input and snapping help make spacing and rotation deliberate.
- Review pattern preferences: options include merging nearby atoms, adjusting hydrogen atoms, and grouping or combining generated structures with existing ones.
After creating the tube, minimize the geometry to relax it, and optionally add hydrogens. Pattern construction establishes the repeated arrangement; minimization is a separate step for refining the resulting structure.
This ring-then-stack approach is useful whenever a molecular model can be built from a repeatable unit. For more details on linear, circular, and curved patterns, see the SAMSON pattern creation guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.