Duplicating Molecular Structures Without Scripts or Spreadsheets

As molecular modeling projects grow in complexity, manually duplicating and arranging molecular structures can quickly become tedious. Whether you’re assembling a nanotube from scratch or building repeating motifs in materials science or biomolecular models, the goal is the same: replicate structures precisely and efficiently. But how?

The Pattern Editors in SAMSON simplify this process dramatically by letting you create linear, circular, and curved patterns directly from selected atoms or groups, using visual on-screen widgets. Here’s how they work — and why they can save you hours of work.

What Are Pattern Editors?

SAMSON includes three specialized editors for pattern creation:

Linear Pattern Editor (Shortcut: L)
Circular Pattern Editor (Shortcut: W)
Curved Pattern Editor (Shortcut: Q)

Each provides interactive 3D widgets to control duplication — with handles to drag, sliders, fine numerical input, and snapping options for precision. You can quickly replicate functional groups, rings, or whole molecules to build complex architectures.

How It Solves Common Modeling Problems

If you’ve been copying and pasting molecular structures to repeat them in space, you likely know the pain of misalignments, missed bonds, and tedious manual adjustments. Pattern Editors address exactly that:

Align structures precisely in desired directions (e.g., stack rings along the z-axis).
Create repeating circular motifs (e.g., close rings aligned on either plane).
Build helices or curved arrangements using the Curved Pattern Editor.

These patterns are common in carbon-based nanostructures, biological polymers, and supramolecular assemblies.

Step-by-Step: Building a Custom Nanotube

Here’s an example of using multiple pattern editors to replicate a common nanostructure manually: a carbon nanotube.

Create a carbon ring manually in the editor and remove its hydrogen atoms.
Align the ring flat on the desired plane using Edit > Align.
Activate the Circular Pattern Editor with W:

Set number of instances (e.g., 12) to form a closed ring.
Adjust radius and orientation so edges connect precisely.

Accept the result to merge overlapping atoms into a proper ring.
Use the Linear Pattern Editor with L to stack the ring along an axis:

Set translation (e.g., 2 Å) and rotation if needed between repeats.
Add as many copies as needed to create the desired tube length.

Minimize the final structure to relax geometry and fix atom placements.

This method gives you full control over spacing, alignment, and geometry in a way that importing pre-built structures or scripting often does not — especially useful when modeling custom architectures.

Precise Control When You Need It

The Pattern Editors go beyond drag-and-drop:

Hold Ctrl (Windows/Linux) or Cmd (Mac) and click widgets to enter exact rotation or translation values.
Activate snapping to enforce fixed spacing or angles.
Use the mouse wheel to adjust the number of copies in real time.

This is especially helpful when replicating motif units in periodic structures or fine-tuning alignments for covalent bonds.

Visual Feedback = Fewer Surprises

Each editor displays live updates in the viewport as you tweak parameters, so there’s no guesswork in how your structure will look. And with the option to automatically merge atoms on overlap and adjust hydrogen atoms during pattern creation, the entire process stays chemically meaningful.

Explore More

Want to fine-tune your patterns further? You can also:

Edit preferences for how atoms merge or how output structures are grouped.
Use Edit > Align / Distribute to further organize your geometry.

Pattern Editors are a great example of how graphical tools can replace clunky secondary approaches — and help modelers focus more on ideas than repetitive tasks. To learn more, visit the SAMSON Pattern Creation documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.