When You Don’t Want It All to Move: How to Minimize Only a Part of a Molecule in SAMSON

When working with complex molecular systems, making small local changes—like adjusting the geometry of an active site or repositioning a functional group—often doesn’t require a full minimization of the entire molecule. In fact, minimizing the whole structure can be counterproductive, especially when most of the molecule is already well-optimized. Fortunately, SAMSON makes it possible to selectively minimize only parts of your molecule, thanks to the freeze and unfreeze functionality built into its Interactive Minimizer Editor.

Here’s how you can control exactly which atoms to minimize, so the rest of your structure stays put. This approach can save time and preserve regions you don’t want to disturb.

Why freeze atoms?

Let’s say you’re tweaking a ligand geometry before docking, or you’ve made a substitution in a small region of a protein and only want to relieve local strain. Freezing atoms prevents them from being affected during minimization, letting you focus the optimization only where it’s needed.

Step-by-step: Partial minimization

  1. Freeze the atoms you want to keep fixed.
    First, select the entire molecule (or leave the selection empty to target the whole document), then go to Edit > Freeze. This marks all atoms as frozen and visually applies a dark blue overlay in the viewport to indicate their fixed status.
  2. Select the atoms you want to minimize.
    Use any selection tool to pick the region where you want to carry out the minimization. This could be a side chain, a loop, or just a few atoms.
  3. Unfreeze the selected atoms.
    With these atoms still selected, go to Edit > Unfreeze. This ‘unlocks’ them so they can respond to the minimization process.
  4. Minimize.
    Activate the Minimizer by clicking Edit > Minimize or using the shortcut key Z. The unfreezed atoms will move while the rest of the structure remains fixed.
  5. Finalize the minimization.
    Click Edit > Minimize again to stop the process. You can optionally unfreeze the whole system using Edit > Unfreeze if needed.

The interactive minimization preferences

What to look out for

It’s important to understand that SAMSON minimizes the entire connected component of your selection. So if you choose an atom that is part of a larger bonded network, the whole structure connected to it will be involved in the minimization unless other parts are frozen first. This makes the freeze/unfreeze method an essential step for true partial minimizations.

Want to see it in action?

Check out this short video demonstrating a partial minimization where frozen atoms are left untouched:

To learn more features, conditions, and tips for effective minimizations, visit the official documentation page on minimization in SAMSON.

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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