When working with molecular models, sometimes you need to refine just a portion of a molecule without affecting the rest. Whether you’re adjusting a ligand conformation within a binding site or optimizing a flexible side-chain, it’s common to want precise control over what gets minimized. This can be challenging in many molecular modeling environments where minimization often affects the entire structure by default.
In SAMSON, you can interactively minimize only part of a molecule with a built-in feature that allows you to freeze atoms. This can help you target your geometry optimizations without disrupting other parts of the system you’ve already refined. Here’s how it works.
Minimizing a Part of a Molecule
The SAMSON Minimizer tool uses the Universal Force Field (UFF) by default for real-time, interactive minimization. Normally, this affects all atoms in the document, but with the use of freezing, you can select exactly which atoms you want to keep static or allow to move.
Step-by-step guide
- Start by using the selection tool to select the whole molecule, or keep the selection empty to affect the entire system.
- Next, go to Edit > Freeze. This will freeze all atoms in your selection. If no atoms are selected, this will freeze the entire molecule.
- Select only the atoms in the part of the molecule you wish to minimize.
- Click Edit > Unfreeze to unfreeze this specific subset of atoms. These atoms are now free to move during minimization.
- Click Edit > Minimize (shortcut: Z) to begin the interactive minimization.
- As soon as you’re done, hit Edit > Minimize again to stop, and optionally unfreeze the rest of the system by clicking Edit > Unfreeze with either the whole structure or nothing selected.
Frozen atoms are visually marked with a dark blue overlay in the SAMSON viewport, helping you keep track of which parts are static during minimization:
Why Freeze?
This selective minimization approach is especially useful in several contexts:
- Focused design: Tweaking a fragment in a ligand or side chain while keeping the global conformation intact.
- Speed: Minimizing only what matters saves computational time and visual overcorrection.
- Interactive modeling: When moving atoms manually with editors, you can then locally relax the region you modified.
To visualize this technique in action, check out this short example video where frozen atoms stay fixed during a partial minimization run:
By mastering this simple yet powerful technique, you can dramatically improve your molecular modeling workflow in SAMSON. It ensures changes are targeted and preserves the structural context you’ve built up to that point.
To learn more about other minimization features, visit the official documentation here: 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.