How to Minimize Only Part of a Molecule in SAMSON Without Affecting the Rest

If you’re modeling complex systems, you’ve probably faced this situation: you just need to adjust a small portion of a molecule—maybe a side chain or a linker—and you don’t want the rest of the structure to move. But most minimization tools apply changes to the whole system, which can be inefficient and even disrupt the parts you want to keep fixed.

Luckily, SAMSON offers an easy solution: selective geometry optimization using atom freezing. This method lets you stabilize or edit just part of a structure without altering the surrounding geometry. Here’s how it works.

Why Minimize Only a Part?

Partial minimization can be helpful in several scenarios:

  • Fixing bond angles or clashes in a local region
  • Modifying ligands or binding pockets in large biomolecules
  • Preparing specific conformers in a bigger structure
  • Speeding up the optimization process

Freezing Atoms: The Key to Local Minimization

SAMSON uses an interactive minimizer that, by default, optimizes all atoms. However, if you want to restrict the minimization to a subset of atoms, you can freeze the other atoms so their positions stay constant.

Step-by-Step Guide:

  1. Select the whole molecule (or leave the selection empty if you want to freeze everything).
  2. Click Edit > Freeze to freeze the selected atoms or the entire structure.
  3. Select the atoms you wish to optimize.
  4. Click Edit > Unfreeze to unfreeze the selected atoms.
  5. Click Edit > Minimize to start the interactive minimization process.
  6. Click Edit > Minimize again to stop minimization once done.
  7. Click Edit > Unfreeze with the structure selected or no selection to unfreeze all atoms.

Atoms that are frozen will remain fixed during minimization and are shown with a dark blue overlay in the viewport, so you can easily distinguish them from movable atoms.

The interactive minimization preferences

Here’s a great video example demonstrating how minimization works with atom freezing:

Good to Know

  • You can combine this approach with SAMSON’s editors for real-time feedback on structural changes.
  • Freezing and unfreezing does not alter atom properties—it only affects whether their positions are included in the minimization process.
  • This workflow is ideal for large molecular systems where full minimization could be time-consuming or computationally expensive.

To learn more, see the full documentation page on minimization in SAMSON: https://documentation.samson-connect.net/users/latest/minimizing/

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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