How to Control Molecular Fragment Orientation in SAMSON

When building molecular structures, one of the recurring challenges for molecular modelers is precisely controlling how fragments connect — especially when assembling complex molecules. Poorly oriented fragments can lead to atomic clashes, unrealistic geometries, or tedious manual corrections. Fortunately, SAMSON provides intuitive tools for orienting fragments and rotating molecular parts, saving a lot of time during model setup.

This post explores how to interactively position and orient fragments while building molecules in SAMSON. It’s a small feature with a large impact: better molecular assemblies, faster workflows, and fewer frustrations. 🔍

Interactive Fragment Orientation: Why It Matters

When you’re combining fragments (e.g., ligands into active sites, small molecules into polymers, or nanoparticle attachments), orientation matters a lot. If fragments overlap atoms or are misaligned, you might end up spending time cleaning up or navigating errors during simulations.

In SAMSON, you can control and modify fragment orientations both before and after placement using simple mouse interactions and edit tools built right into the Viewport. Here’s how.

Setting the Pivot and Using Move Editors

Whether you’re adding functional groups to a molecule or composing supramolecular assemblies, SAMSON provides Move editors that let you adjust orientation after inserting a fragment:

  • Press M to activate the Local Move Editor.
  • Select the fragment you want to move. Just added a new one? It should already be selected.
  • Zoom in and click on the pivot atom – the rotation center – to rotate around a specific point.

Then, use the on-screen controls: drag the sphere to rotate in 3D freely, or use axis-aligned arrows for precise rotation along X, Y, or Z.

Orienting a fragment of a molecule

Rotation Around Bonds

You can also rotate specific parts of a molecule around individual bonds (like rotating a side chain or conformationally exploring a torsion angle):

  • Press M to activate the Local Move Editor again.
  • Click on the bond you’d like to rotate around.
  • SAMSON selects the shortest fragment connected through the bond and displays rotation controls.

This is particularly useful in modeling rotamers, sampling conformational space, or preparing input for docking workflows.

Build Symmetry and Order into Structures

Want to create multiple copies of a structure positioned radially or on a grid? SAMSON allows you to copy and rotate structures using the Global Move Editor (shortcut: K). Set up your desired symmetry by combining pivot points with angular snapping (useful for nanostructures, molecular cages, and more).

Extra Tips

  • Hold Shift + right-click before fragment placement to rotate the fragment interactively in the Viewport.
  • Enable Snapping options in the top-left of the Viewport if you want fragments added at specific orientations or distances.
  • Pair fragment orientation with interactive minimization (Z) to see your fragment relax during placement.

A little control over orientation goes a long way—and SAMSON’s tools make it smooth without requiring scripting or manual coordinate adjustments. Ready to streamline your assembly process and make cleaner models?

You can learn more about molecular building tools in SAMSON here.

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

Comments are closed.