How to Precisely Control Fragment Orientation When Building Molecules

When modeling complex molecular structures, one of the most common — and frustrating — pain points for molecular modelers is achieving the precise spatial arrangement of molecular fragments. Whether you’re building ligands, assembling macromolecular complexes, or preparing simulation-ready systems, accurate fragment orientation can significantly affect the validity and usefulness of the model.

SAMSON, the integrative molecular design platform, provides several tools to make this process easier and more controlled. In this post, we’ll explore how SAMSON helps you orient molecular fragments with precision — whether you’re setting up symmetrical assemblies or replacing chemical groups — and how these tools interact with other features like snapping and minimization.

Changing the Orientation of Fragments on the Fly

After inserting a fragment, you might realize its default orientation isn’t quite what you expected. Fortunately, SAMSON allows you to reorient fragments interactively using Move editors. The most frequently used is the Local Move Editor (M key shortcut), which provides rotation and translation controls directly in the viewport.

To reorient a newly added fragment:

  • Activate the Local Move Editor (M).
  • Select the fragment in the viewport.
  • Click on an atom in the fragment to set it as a rotation pivot.
  • Use the sphere interface to rotate the fragment in any direction.

This makes it possible to align fragments relative to specific bonds, match spatial geometries, or create regular patterns in molecular assemblies.

Orienting a fragment of a molecule

Building Symmetrical Systems

SAMSON also includes a Global Move Editor (K) that allows you to rotate and place entire molecular units. Combined with rotational snapping, this is a powerful way to build symmetrical systems like ring assemblies or multimeric complexes.

For example, you can:

  • Duplicate a molecule.
  • Set a pivot atom (around which to rotate).
  • Apply rotational snapping to control discrete angular steps.

Here’s how it looks in action:

Rotating Around a Specific Bond

One of the most interesting ways of reorienting a fragment is to rotate it around a specific bond — which is remarkably easy in SAMSON. Simply click on the bond while the Local Move Editor is active, and SAMSON will automatically select the smaller fragment and show interactive rotation tools.

This is particularly useful when adjusting torsion angles or exploring different conformations:

Tips for Better Control

To streamline the process, consider the following:

  • Turn off snapping during precise positioning. It can be helpful for grid-aligned placement but may interfere in free-form design.
  • Use interactive minimization (Z) after placement to improve geometry without manually tweaking bond lengths or angles.
  • Hold Shift while adding a fragment to choose exactly which atom and bond it will use for substitution.

Whether you’re modeling small molecules or large assemblies, mastering fragment orientation in SAMSON opens up fine control over structure construction — all while keeping the process interactive and intuitive.

To explore in more detail, visit the full SAMSON documentation on fragment orientation.

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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