Why Your Molecular Fragments Aren’t Fitting Correctly (And What to Do About It)

When building molecular models, especially large or branched structures, one of the common frustrations for chemists and molecular designers is accidentally placing fragments too close, overlapping atoms, or misaligning critical functional groups. Even with care, fragment orientation can be tedious and time-consuming to correct manually.

Fortunately, in SAMSON, you don’t have to struggle with aligning every atom by hand. Whether you’re constructing with small fragments or assembling entire biomolecular models, the platform offers several intuitive tools to help you place and orient fragments more accurately—and efficiently.

How Fragment Placement Works in SAMSON

By default, SAMSON uses intelligent orientation tools to help you assemble molecules in 3D:

  • Predictive orientation: When placing a new fragment, SAMSON automatically adjusts its position to minimize overlap with atoms already present in the model.
  • Hydrogen adjustment: Added fragments update neighboring hydrogen atoms based on valence rules, saving time and preserving chemical logic.
  • Forbidden substitution detection: The software displays a green overlay for allowed placements and a red overlay for disallowed ones. That means no accidental misplacement.

These features are enabled in the builder preferences. Make sure to check:

Enable the following options for optimal behavior:

  • Automatically orient fragments on substitution
  • Prevent unexpected substitutions
  • Merge neighboring atoms

Rotating Fragments Manually

Sometimes, you might want finer control beyond automated suggestions. For example, aligning carbohydrates or adding bulky groups like phenyl rings at specific angles. For that, SAMSON offers the Local Move Editor.

To activate this editor:

Then, click on the fragment to display rotation and translation controls. Use these to:

  • Rotate fragments using a trackball-like interface.
  • Set a specific atom as the pivot for rotation.
  • Move the fragment without breaking pre-defined bonds.

Orienting a fragment of a molecule

Rotating Around Bonds

If you need to adjust the torsion around a bond—say you’re trying to minimize steric hindrance or optimize interaction sites—you can simply:

  1. Activate the Local Move Editor (M).
  2. Click on the bond directly.
  3. Use the move controls to rotate around the selected bond.

This is especially useful in drug design and conformational analysis where subtleties in 3D structure matter.

Building with phenol asset

Troubleshooting Tips

  • Fragments not positioning correctly? Check if “Automatic orientation” and “Merge neighboring atoms” are enabled in preferences.
  • Too much overlap or strange positions? Turn off Snapping options in the viewport’s top-left corner for free placement.
  • Prefer full manual control? Disable predictive placement entirely and use move editors alongside interactive minimization (Z) for real-time geometry updates.

Orienting fragments well saves downstream editing time and ensures structurally meaningful models from the start.

📚 To explore all builder tools and orientation features, visit the original documentation: https://documentation.samson-connect.net/users/latest/building-molecules/

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

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