Building a long molecular structure one unit at a time is tedious—and small placement errors can accumulate as you go. Carbon nanotubes are a good example: the tube is made from repeated units, but arranging those units consistently by hand can be difficult. A more manageable approach is to build a ring first, then use pattern editors to repeat it.
In SAMSON, the Circular and Linear Pattern Editors provide interactive ways to duplicate a selected structure. The workflow below uses a carbon ring as a starting point. The same general idea—make one useful unit, arrange it into a larger shape, then extend the shape—can help with other repeated molecular architectures too.
1. Prepare a repeatable unit
Create a ring and remove its hydrogen atoms. Then rotate the ring so its edges are oriented as needed for the intended connections. This preparation matters: a pattern editor repeats the structure you select, so the orientation of that first unit determines the arrangement of its copies.
Before duplicating anything, select the ring structure you want to repeat. If the selection or orientation is not what you intended, the pattern will faithfully repeat the wrong starting setup. Taking a moment to check the unit can save time later.
2. Close the ring with circular repetition
Activate the Circular Pattern Editor with W. Increase the number of instances—for example, try 12—and adjust the radius until neighboring edges line up as intended. The editor provides an interactive widget for positioning and adjusting the pattern, with live visual feedback.
When the arrangement looks right, accept it. The documentation describes accepting the pattern to merge overlapping atoms into a single ring. Pattern behavior can also be fine-tuned in Preferences > Edit > Create pattern (circular / curved / linear), including whether nearby atoms are automatically merged. Check these settings if the result does not behave as expected.
3. Align the ring, then extend it
Align the completed ring—for example, to the XY plane—using Edit > Align. A consistent orientation makes the next step easier to reason about: the Linear Pattern Editor will repeat the ring along a direction, such as the Z-axis.
Activate the Linear Pattern Editor with L. Adjust the translation between copies; 2 Å along Z is an example from the workflow, not a universal spacing value. If needed, set an incremental rotation between copies to help match the arrangement. The widget lets you adjust the pattern interactively. For precise values, hold Ctrl on Windows or Linux, or Cmd on macOS, and click a widget. You can also set snapping to control translation distances and rotation angles.
To change how many copies are previewed, scroll while hovering over the central widget. Holding Ctrl or Cmd while scrolling changes the copy count more quickly. Inspect the displayed arrangement before accepting it; spacing and orientation are choices to verify for your particular structure.
4. Finish by checking the geometry
After accepting the linear pattern, minimize the structure to relax its geometry. Hydrogens can also be added if needed. Patterning creates the repeated arrangement, but the resulting structure should still be checked and prepared for the next stage of your modeling workflow.
A useful way to think about pattern building
Instead of placing every part of a large structure individually, separate the task into two questions: what is the repeatable unit, and how should that unit be arranged? For this nanotube example, the ring is the unit, circular repetition assembles it into a ring-shaped structure, and linear repetition extends that structure into a tube. The same approach can make repeated architectures easier to construct and revise.
For editor shortcuts, controls, preferences, and the full nanotube example, see the SAMSON guide to creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.