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

Many molecular modelers run into the same problem when trying to refine a local geometry: they want to minimize just part of a molecule without affecting everything else. Say you’ve modified a side chain, added a ligand, or just built a new fragment—you don’t want to reoptimize the whole system, which might already be in a near-optimal state.

In SAMSON, this can actually be handled easily and interactively using the freeze/unfreeze functionality. This method allows you to minimize only selected atoms while keeping the rest fixed. In this blog post, we’ll walk through how to do this step-by-step, with tips and visual aids to guide you along the way.

Why Freeze?

When you’re doing interactive minimization using the Universal Force Field (UFF) in SAMSON, every atom is generally optimized if it belongs to the active document. That’s fine in many cases, but what if you only want to relax a changed region while keeping the rest of your molecule or complex intact?

This is where freezing comes in: it lets you prevent parts of your structure from being affected by the optimization process. Here’s how.

Minimizing a Subset of Atoms

Select the full molecule (or leave the selection empty if you want to freeze the whole document).
Go to Edit > Freeze to fix these atoms in space. A dark blue overlay in the viewport will indicate frozen atoms.
Select the part of the molecule you actually want to minimize (such as a specific residue or group).
Go to Edit > Unfreeze to make only this selection movable.
Click Edit > Minimize (shortcut: Z) to start the interactive minimization.
Move atoms, if needed, to help them find local minima faster, or simply let SAMSON relax them into place on its own.
Click Edit > Minimize again to stop.
If you’re done, go to Edit > Unfreeze with nothing selected to unfreeze the whole structure.

This offers a clean, precise approach to local geometry improvement without introducing changes elsewhere in your model.

Quick Tip

Even if you select just one atom in a molecule, SAMSON will still minimize the whole connected component of that atom. To isolate a region, you must freeze everything else and selectively unfreeze only the part you’re interested in.

Visual Example

Here’s a screenshot from the documentation showing the preferences section where you can tweak minimization settings:

To see this workflow in action, check out the example video embedded in the original documentation showing how freeze/unfreeze operations allow you to control what gets minimized.

This functionality really shines when working on complex systems or during iterative model building. You can minimize a residue after mutating it, clean up a binding pocket, or stabilize a modeled loop—all without disturbing the rest of your work.

To learn more, visit the original documentation page on minimization: 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.