Precisely Orient Molecular Fragments in SAMSON for Cleaner Models

When building molecular systems, precise positioning of fragments can make or break your simulations. Whether you’re assembling a drug molecule using building blocks or tweaking the conformation of a ligand bound to a receptor, intuitive control over fragment orientation avoids clashes and reduces clean-up later. 💡

SAMSON, the molecular design platform, offers powerful tools to orient fragments interactively and efficiently. This blog post dives into those tools, helping you save time and streamline structural model creation.

Why fragment orientation matters

Rotating pieces of a molecule manually can be time-consuming and imprecise. Misaligned fragments can introduce nonphysical bond angles, steric overlaps, or simply confuse collaborators. If you’re building complex systems from recurring fragments — such as sugars, aromatic rings, or ligands — placing them cleanly from the start makes future tasks easier: force field minimization, docking, MD setup, and more.

Local Move Editor: rotate with precision

To orient a new fragment right after adding it, SAMSON’s Local Move Editor shines.

  1. Press M to activate the Local Move Editor.
  2. Select your fragment. If it was just added, it may already be selected.
  3. Zoom in and click on the atom you want to use as a pivot.
  4. Then, drag the on-screen widget to rotate around that pivot interactively.

This is especially useful for aligning glycosidic bonds, stacking rings, or matching angles from experimental data.

Orienting a fragment of a molecule

Global Move Editor: replicate with symmetry

If you want to place multiple copies of a substructure (e.g., a monomer around a central hub), activate the Global Move Editor by pressing K. You can set pivot atoms and use rotational snapping to automate symmetric placements and distribute fragments evenly.

This editor is ideal for placing fragments around binding pockets, creating supramolecular structures, or modeling nanostructures with defined geometry.

Rotate around bonds with a click

Want to rotate around a bond connecting two fragments? With the Local Move Editor active, simply click the bond. SAMSON automatically selects the shortest connected piece and enables rotation widgets around that axis.

It’s a fast way to adjust dihedrals or explore conformational space before simulations.

Best practices

  • Use Z to activate interactive minimization when rotating — this keeps your structure energy-minimized as you make changes.
  • Snapping controls are available in the top-left corner of the viewport if you want grid-based adjustments.
  • You can always undo steps via Edit > Undo (Ctrl+Z).

A well-positioned fragment goes a long way in maintaining clean documentation and preparing for downstream operations. The tools in SAMSON make this intuitive and adaptable to your modeling needs.

To explore these features in detail, visit the original documentation page: Building molecules in SAMSON.

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

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