Minimizing Only a Part of a Molecule in SAMSON: A Better Way to Adjust Structures

A common challenge in molecular modeling is the need to make small, precise changes to a structure without affecting the overall geometry. Whether you’re adjusting a functional group, refining a ligand conformation, or modifying only part of a large system, you sometimes want to minimize only a region of a molecule while leaving the rest untouched.

SAMSON provides a flexible way to handle this through interactive minimization with selective freezing. This allows you to keep specific atoms fixed while minimizing only the subset you care about.

Why minimize a part of a molecule?

In many real-world scenarios, you may want to:

Optimize a binding site without altering the rest of the protein.
Adjust molecular fragments before merging them into a larger system.
Relax strained geometries caused by manual editing.

Traditional minimization would involve recalculating the entire structure. But that’s often inefficient and may inadvertently disturb regions that were already well-optimized.

How to minimize a part of a molecule in SAMSON

SAMSON’s interactive minimizer combined with freezing enables this precise control. Here’s a quick step-by-step guide:

Select the full molecule or leave the selection empty.
Click Edit > Freeze to freeze the selection — this tells SAMSON to exclude these atoms from the minimization.
Select only the atoms you want to minimize.
Click Edit > Unfreeze to unfreeze the selected atoms — now they are free to move during minimization.
Click Edit > Minimize to start the interactive minimization.
Click Edit > Minimize again to stop it when you’re satisfied.
Finally, click Edit > Unfreeze again (with nothing or the molecule selected) to reset everything.

This technique gives you local control — without leaving the interactive environment — making it especially useful for iterative design work or small adjustments during molecule building or docking.

Visual cues and tips

Frozen atoms are displayed with a dark blue overlay in the SAMSON viewport, so it’s easy to see which regions are active or fixed. This is great for double-checking before launching a minimization. Keep in mind that when selecting individual atoms, SAMSON automatically includes the whole connected component, so freezing is helpful if you want to narrow down edits with more precision.

To learn more, watch the short demo video in the documentation that shows how frozen atoms behave during minimization.

Final thoughts

This feature is particularly helpful for researchers who model large systems but need to make local changes frequently—proteins, materials, or even complex supramolecular assemblies. It saves time and avoids unexpected distortions elsewhere in the structure.

To learn more, visit the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.