Building Smart: How to Orient Molecular Fragments Precisely in SAMSON

For many molecular modelers, a frequent source of frustration is getting that one fragment to align just right. Whether assembling a ligand into a binding pocket or fusing building blocks into nanostructures, orientation matters. A slight misalignment can mean hours of tedious rotation and repositioning—or worse, starting over.

Thankfully, SAMSON offers practical, user-friendly solutions to help modelers gain precision and save time when orienting molecular fragments during the model-building process. Here’s how to take advantage of these tools to make your molecular modeling workflow more efficient.

Choosing the Right Tool: Local vs. Global Move Editors

In SAMSON, positioning fragments precisely is possible thanks to the Move editors. Two commonly used editors are:

  • Local Move Editor (M): Best when moving or rotating individual fragments.
  • Global Move Editor (K): Ideal for rotating or aligning multiple structures around a pivot point.

Using the Local Move Editor for Fine Orientation

Position a newly added fragment exactly the way you want by activating the Local Move Editor and selecting the fragment. To refine the orientation:

  1. Zoom in to clearly see the atoms in your structure.
  2. Click a specific atom in the fragment to set it as the pivot point for rotation.
  3. Click and drag the interactive controls (spherical handles or arrows) to rotate or move the fragment accordingly.

This tool is particularly helpful when connecting functional groups or aligning charged regions. It offers visual control and avoids relying solely on manual coordinate input.

Orienting a fragment of a molecule

Rotating Around a Bond

To rotate a portion of a molecule around a bond—such as moving a side chain or rotating a ring system—you can:

  1. Activate the Local Move Editor.
  2. Click directly on the bond you want to rotate around.
  3. SAMSON identifies the smallest fragment on either side and displays rotation controls.
  4. Drag the controls to adjust the torsion angle precisely.

This is especially convenient when optimizing geometries or checking for plausible conformations in ligand frameworks or chain extensions.

Changing bond order

Arranging Structures with the Global Move Editor

When working with larger assemblies like symmetrical nanomaterials, multi-component systems, or arrays of repeating units, the Global Move Editor speeds up the positioning process.

You can:

  • Select all the structures you want to rotate.
  • Choose a pivot atom to rotate around a specific center.
  • Enable snapping for angular precision, ensuring your components align consistently.

This editor is especially useful to arrange fragments symmetrically—as shown in the example below where fragments are copied and distributed around a central structure with precision:

Tips for Better Orientation Workflow

  • Switch on Node details at the bottom of the Viewport to display atom names while hovering.
  • Use Shift + right-click to rotate fragments freely during substitution.
  • Use Ctrl or Cmd + click to select the substitution atom in a fragment before inserting it.

The combination of interactive visual aids and control tools in SAMSON makes the orientation process far more intuitive and precise. Whether you’re working on a single ligand or a periodic nanostructure, you can align and rotate your molecular components with confidence and efficiency.

To explore more about fragment orientation and other smart building workflows, visit the full documentation page: https://documentation.samson-connect.net/users/latest/building-molecules/

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

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