Building a nanotube from molecular pieces can be tedious for a simple reason: every copy must be positioned and oriented consistently. Small placement errors can leave gaps or overlapping atoms, while repeating the same manual move many times makes the process slow and difficult to reproduce.
In SAMSON, you can approach this task in two stages: first arrange a molecular ring into a closed circle, then repeat that ring along an axis. The circular and linear Pattern Editors handle the duplication and transformation, while snapping and precise-value controls help you tune the geometry.
1. Prepare a ring that can connect
Create a ring structure, remove its hydrogen atoms, and rotate it so its edges are oriented appropriately for connection. This preparation matters: the pattern tools duplicate the structure you select, so they will reproduce its orientation and any atoms it contains. Select the ring before activating a Pattern Editor.
If you are new to building and selecting structures in SAMSON, the Building molecules and Selecting guides cover those basics.
2. Close the ring with the Circular Pattern Editor
Activate the Circular Pattern Editor with W. Adjust the number of instances—12 is one example from the workflow—and change the radius until neighboring edges line up. The editor provides an on-screen widget with live visual feedback, so you can inspect the arrangement before committing to it.
Use the mouse wheel over the central widget to change the number of copies. For a faster change, hold Ctrl on Windows or Linux, or Cmd on macOS, while scrolling. Drag the widget handles to adjust the arrangement interactively. When you need a specific transformation, hold the same modifier and click a widget to enter precise translation or rotation values. Snapping can help control translation distances and rotation angles.
Once the instances form the intended circle, click Accept. If nearby atoms should be merged, check the pattern-creation preferences before committing: SAMSON provides an option to automatically merge nearby atoms. The outcome depends on the chosen geometry and settings, so inspect the result rather than assuming every connection is correct.
3. Align the ring, then extend it
Align the completed ring—for example, to the XY plane—using Edit > Align. The orientation you choose establishes the direction in which the next pattern will grow. Then select the ring and activate the Linear Pattern Editor with L.
Set the translation along the Z-axis; 2 Å is an example spacing in the documented workflow. If the copies need a twist to match their edges, specify an incremental rotation between them. You can use the widget for a quick visual adjustment or enter values for more controlled placement. Adjust the number of copies with the mouse wheel over the central widget, then review the preview for spacing and alignment before accepting.
This two-step construction separates two different geometric decisions: the circular editor sets the circumference, and the linear editor sets the length. If the ring is not aligned or its neighboring edges do not meet as intended, resolve that before creating a long stack; otherwise the same mismatch will be repeated through the structure.
4. Inspect and refine the result
After accepting the linear pattern, inspect the extended structure and minimize it to relax its geometry. You can optionally add hydrogens as part of the later refinement. Pattern preferences also let you choose whether generated structures are grouped or combined with existing ones, and whether hydrogen atoms are adjusted. These choices are useful to check when planning how you will continue working with the model.
The same editors support other repeated arrangements, not only nanotubes: linear, circular, and curved patterns can help assemble larger structures from selected atoms, molecules, or other structural units. The core workflow remains the same: prepare and select the source, choose the pattern shape, set copy count and transformations, inspect the preview, and accept when the arrangement is right.
For a visual walkthrough, see the SAMSON guide to creating patterns, which includes a nanotube tutorial and additional details on pattern controls.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.