Building a repeated molecular structure by hand can quickly become a tedious cycle: duplicate a molecule, move it, rotate it, check the spacing, and repeat. Small inconsistencies can accumulate, and arranging many copies manually makes it harder to keep the overall geometry under control.
SAMSON’s pattern editors offer a more systematic approach. Start with a structure you have built or loaded, select the part you want to repeat, then use a linear, circular, or curved pattern to place copies with interactive controls and live visual feedback. This is useful whenever the main challenge is not creating one molecular unit, but arranging many units consistently.
Choose a pattern that matches the structure
- Linear pattern (L): Repeat a structure along a line—for example, to extend a chain or stack repeated units.
- Circular pattern (W): Arrange copies around a center, such as when assembling a ring.
- Curved pattern (Q): Follow a curve when a straight line or circle does not fit the shape you need.
You can open these editors from the Editors Toolbar beside the viewport or find them using the “Find everything…” bar. The shortcuts are handy once you know which editor you want, but the toolbar is a useful place to start if you are still exploring.
A practical workflow for repeatable placement
- Prepare the unit. Build or load the molecule or structure you want to duplicate. Select the intended atoms or structure before activating a pattern editor.
- Choose the pattern type. Activate the linear, circular, or curved editor that fits the arrangement you are aiming for.
- Set placement and orientation. Drag the on-screen handles to adjust the copies. For more precise translation or rotation values, hold Ctrl on Windows or Linux, or Cmd on macOS, while clicking a widget. Snapping can help keep translations and rotation angles at consistent intervals.
- Set the number of copies. Hover over the central widget and scroll the mouse wheel. Hold Ctrl or Cmd while scrolling to change the copy count more quickly.
- Review before accepting. Check the spacing, orientation, and overall shape in the viewport. When the arrangement is ready, click Accept to finalize it.
This separation between preparing the building block and arranging its copies is a useful way to reduce repetitive manual work. It also makes it easier to adjust the pattern interactively before committing to the result.
Example: assembling a nanotube from rings
A carbon nanotube illustrates how two pattern types can work together. Begin by creating a ring, removing hydrogen atoms, and rotating the ring so its edges are aligned as needed. With the Circular Pattern Editor, increase the number of instances—for example, to 12—and adjust the radius until the edges line up. Accept the result to merge overlapping atoms into a single ring.
Next, align the ring, for example to the XY plane, and use the Linear Pattern Builder to stack copies along the Z-axis. Adjust the translation between rings (the documentation gives 2 Å as an example) and add an incremental rotation if needed to match the bonds. Accept the pattern to create the tube, then minimize the geometry to relax it; hydrogens can optionally be added afterward.
The key idea is to solve the geometry in stages: first make a suitable ring, then repeat it into a larger structure. If the result is not aligned as expected, revisit the ring orientation, radius, spacing, or rotation rather than trying to correct every copy individually.
Keep the result organized
Pattern preferences are available under Preferences > Edit > Create pattern (circular / curved / linear). Options include automatically merging nearby atoms, adjusting hydrogen atoms, and choosing whether generated structures are grouped or combined with existing ones. For additional organization after pattern creation, use Edit > Align / Distribute to align structures by origin, axis, or compass planes, or distribute them evenly in chosen directions.
For a visual introduction, SAMSON’s interactive tutorials cover working with documents, selecting in the viewport, building with atoms, and moving objects. The image below is from the “Building with atoms” tutorial.
For more details and the video tutorials, see the SAMSON guide to creating patterns.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.