How to Tweak Just Part of a Molecule in SAMSON

When working with complex molecular systems, it’s not always necessary (or desirable) to optimize the whole structure. Whether you’re fine-tuning a ligand inside a binding pocket or just adjusting a fragment of a large biomolecule, minimizing only a specific region can save time and preserve the structure of other parts of the system. In SAMSON, this is easy to achieve using the Freeze and Unfreeze tools. Here’s how it works.

Why partial minimization?

Sometimes, you don’t want to disturb the full geometry—perhaps you’ve already arranged your protein backbone carefully or you’re working inside a constrained binding site. Full minimization might lead to undesirable rearrangement. Instead, you can freeze parts of the molecule to keep them fixed while optimizing only the section you care about.

Freezing regions to control minimization

The concept is simple: atoms that are frozen will stay in place during minimization, while unfrozen atoms will be updated during energy relaxation. Here’s how to use this approach in SAMSON:

  1. Select the whole molecule (or leave the selection empty to target everything).
  2. Click Edit > Freeze to freeze the atoms in the selection. If nothing is selected, this will freeze all atoms.
  3. Select the part of the molecule you want to minimize.
  4. Click Edit > Unfreeze to allow only the selected atoms to move.
  5. Click Edit > Minimize to begin interactive minimization. Click the same again to stop.
  6. Once done, click Edit > Unfreeze again to unfreeze the rest of the molecule, if needed.

Frozen atoms are visibly indicated in the viewport with a dark blue overlay, so it’s easy to keep track of which atoms are mobile and which are not.

Let’s take a look

This image from the Preferences panel shows the settings that control the behavior of the minimizer:

The interactive minimization preferences

Once you’ve frozen specific atoms, you can selectively tweak parts of the structure in a controlled way. For example, if you’re interested in refining a loop region in a protein or adjusting the conformation of a ligand fragment, this method gives you precise control.

To see this approach in action, check out the short tutorial video below from the documentation page, which demonstrates how to freeze parts of a molecule before minimizing a specific region:

Pro tip

If you only select one atom to unfreeze, SAMSON still considers the entire connected fragment during minimization. That means you can’t minimize just a single atom within a molecule—you’ll need to break connections or split fragments if finer control is needed.

To learn more about partial minimization and other related features in SAMSON, visit the official documentation page.

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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