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Creating patterns#

SAMSON provides a number of powerful ways to build and modify molecular systems thanks to various editors and apps. Among them are the three pattern building editors that let you rapidly replicate and arrange molecular structures in linear, circular, or curved patterns:

  • Linear pattern editor (shortcut: L)
  • Circular pattern editor (shortcut: W)
  • Curved pattern editor (shortcut: Q)

Pattern builders enable fast construction of complex nanoscale architectures and is useful across domains like:

  • Nanotechnology (e.g., nanotubes, nanomachines).
  • Biomolecular modeling.
  • Material science.

Pattern creation supports designing systems with hundreds of thousands of atoms in a few steps, using intuitive and precise controls.

Quick look on pattern creation features#

Video tutorial#

You can learn how to use Pattern Buildes from the following extract of the SAMSON 2025 webinar:

Tips and resources#

We recommend going through the following interactive tutorials (1) integrated into SAMSON that will guide you through the basic operations:

  1. Help > Tutorials
  • "Working with documents"
  • "Selecting in the Viewport"
  • "Building with atoms"
  • "Moving objects in the Viewport"

Interactive tutorial in SAMSON

You can also check the following sections of the User Guide:

  • Selecting

    Learn how to perform selections in SAMSON using commands, filters, editors, scripting, or directly in the document view.

  • Moving around

    Learn how to move around in SAMSON's viewport using mouse or keyboard.

  • Moving objects

    Learn how to move objects in SAMSON using various move editors.

  • Building molecules

    Learn how to build and modify molecular systems using various tools in SAMSON: editors, assets, etc.

Available Pattern editors#

You can access Pattern editors via the Editors Toolbar (left of the viewport) or via the Find everything... bar at the top.

  • Linear pattern editor (shortcut: L)
  • Circular pattern editor (shortcut: W)
  • Curved pattern editor (shortcut: Q)

Each editor provides an interactive widget to position, rotate, and duplicate structures with live visual feedback.

Basic usage steps#

  1. Create or load an atomic structure, then select the structure to duplicate (atoms, molecules, rings, etc.).
  2. Activate a Pattern Editor (Linear, Circular, or Curved).

  3. Position and rotate the duplicated structures using on-screen widgets:

    • Drag handles for interactive transformation.
    • Hold Ctrl (Windows/Linux) or Cmd (macOS) and click widgets to enter precise values for translations and rotations.
    • Set snapping to control translation distances and rotation angles.

  4. Adjust the number of copies:

    • Scroll the mouse wheel while hovering over the central widget.
    • Use Ctrl / Cmd + scroll to change copy count more quickly.

  5. Click Accept () to finalize the pattern.

Advanced controls and preferences#

You can fine-tune pattern behavior in Preferences > Edit > Create pattern (circular / curved / linear):

  • Automatically merge nearby atoms.
  • Adjust hydrogens atoms.
  • Choose whether to group or combine generated structures with existing ones.

Use Edit > Align / Distribute for further structure organization (see Align and distribute structures):

  • Align by origin, axis, or compass planes.
  • Distribute structures evenly across chosen directions.

Example: Creating a linear pattern#

  1. Build a small molecule and minimize it.
  2. Select it and activate the Linear Pattern Editor (L).
  3. Adjust spacing and rotation between replicas.

  4. For precise alignment, click the center of the widget:

    • Set X/Y/Z translations (e.g., 2 Å on Z-axis).
    • Set incremental rotation between copies (e.g., 0°).

  5. Accept () the result to build your extended structure.

Example: Constructing a nanotube manually#

SAMSON provides a Carbon Nanotube Editor that can be accessed via the Editors Toolbar (left of the viewport) or via the Find everything... bar at the top. In the video tutorial we show how you can create a Carbon Nanotube (CNT) using the Pattern Builders, you can follow it with these steps:

  1. Create a ring, remove hydrogen atoms, and rotate to align edges.

  2. Activate the Circular Pattern Editor (W):

    • Increase the number of instances (e.g., 12) to form a closed ring.
    • Adjust the radius to align edges for bonding.
    • Accept () to merge overlapping atoms into a single ring.

  3. Align the ring (e.g., to the XY plane) using Edit > Align (see Align and distribute structures).

  4. Apply the Linear Pattern Builder (L) to stack rings into a tube:

    • Translate along the Z-axis (e.g., 2 Å).
    • Incrementally rotate each replica if needed to match bonds.
    • Accept () to create a tube structure.

  5. Minimize to relax the geometry and optionally add hydrogens.