Freezing Atoms: A Simple Way to Minimize Just Part of a Molecule in SAMSON

When working with complex molecular systems, it’s common to want fine control over what parts of a structure are optimized. Imagine you’re refining only a flexible loop in a protein, or adjusting a ligand’s conformation while keeping the binding site fixed. In such cases, minimizing the whole structure may not only be unnecessary—it might also introduce unwanted changes elsewhere.

This is where SAMSON’s Selective Minimization feature comes into play. With the ability to freeze sections of a molecule, SAMSON lets you minimize just what you need while keeping the rest of your model untouched. This blog post walks you through how to carry out a targeted minimization by freezing atoms in your structure.

Why Freeze Atoms?

Freezing atoms is especially useful when:

  • You want to optimize a local region without disturbing the global structure.
  • You’re working in a multi-step modeling workflow where parts of the structure are already fixed.
  • You’re making incremental changes for step-by-step validation in a publication or report.

Step-by-Step: Minimizing a Selected Region

Here’s how you can minimize just part of your molecule while keeping everything else stable:

  1. Select the entire molecule or keep your selection empty if you want to freeze the whole structure initially.
  2. Go to Edit > Freeze to freeze the selected atoms (or all atoms if nothing is selected).
  3. Select the part of the molecule you’d like to minimize.
  4. Click Edit > Unfreeze to allow only this region to change during minimization.
  5. Click Edit > Minimize to start interactive minimization.
  6. Once done, click Edit > Minimize again to stop the action.
  7. To unfreeze everything, select the molecule (or nothing) and choose Edit > Unfreeze.

The interactive minimization preferences

What Does Freezing Actually Do?

Frozen atoms are excluded from the minimization process: their spatial coordinates remain unchanged. In the SAMSON viewport, they are visually marked with a dark blue overlay, making it easy to distinguish between frozen and active regions.

Things to Keep in Mind

  • To unfreeze only a region, select it and use Edit > Unfreeze. This precise control lets you optimize just a sub-region of interest within a larger system.
  • If you select a single atom to unfreeze and minimize, SAMSON automatically includes the entire connected component (e.g., the whole molecule it belongs to).
  • To minimize smaller fragments (like a side chain or loop), freeze the entire molecule first, then unfreeze only the desired atoms.

Example in Action

If you’d like to see how this works in real-time, SAMSON offers an instructional video showing minimization with frozen atoms. This visual walkthrough clarifies the freezing and unfreezing process and demonstrates the degree of control you can achieve during interactive optimization.

Controlled minimization is a powerful way to preserve structural integrity while refining specific features of your model. The freezing/unfreezing method described here lets you focus on exactly the regions you want to improve.

To learn more about selective minimization and other features, visit the full SAMSON minimization documentation.

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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