When working with complex molecular systems, sometimes you only need to refine a small region of a structure — perhaps an active site, a flexible region, or a newly added side chain. Re-minimizing the entire molecule can be slow and unnecessary.
If you’re using SAMSON for molecular modeling, there’s a simple and effective way to selectively minimize just the part of the molecule you care about: by freezing the rest of the structure.
Why selectively minimize?
There are many reasons why you might want to minimize only a portion of a molecule:
- You added or modified atoms in one area and want to relax just that region.
- You want to preserve the overall geometry of a large macromolecule.
- You only need a local refinement to analyze a specific interaction.
SAMSON allows interactive minimization using the Universal Force Field (UFF). Normally, this affects the whole molecular system, but by using the Freeze tool, you can control exactly which atoms are optimized and which remain fixed.
Step-by-step: Minimizing part of a molecule
Here’s how you can minimize just a part of a molecule in SAMSON:
- Select the entire molecule (or leave the selection empty to apply changes to all atoms).
- Go to Edit > Freeze. This will freeze (fix) the selected atoms, or all atoms if nothing is selected.
- Select the region you want to optimize. Use the selection tools to choose just the atoms or residues you want to minimize.
- Go to Edit > Unfreeze. This will allow only the selected atoms to move.
- Click Edit > Minimize to start the interactive minimization.
- Click the same menu item again to stop the minimization when you’re happy with the result.
- If needed, Unfreeze everything after minimization via Edit > Unfreeze with all atoms selected or no selection at all.
Visual tip: Know what’s frozen
You can easily tell which atoms are fixed: they are overlaid in dark blue in the viewport. This helps avoid confusion, especially in large systems.
Here’s a visual example of how partial minimization can be applied with frozen regions for precise control:
When to use this technique
Partial minimization is especially useful when:
- You’ve made local changes in a stable structure.
- You want to compare the effects of small conformational changes.
- You are preparing a system for further simulation, but only need local adjustments first.
This technique gives you fine-grained control over molecular optimization without having to re-minimize entire systems. Try it out the next time you only need a small tweak in your structure.
To learn more, visit the official documentation page: https://documentation.samson-connect.net/users/latest/minimizing/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.