When modeling molecular systems, it’s not uncommon to need to optimize the geometry of only a part of a molecule — for example, tweaking a binding site while preserving the framework of a protein. However, many molecular modeling platforms default to minimizing the entire molecule or even the whole system. This can unintentionally disturb well-prepared parts of the structure, leading to extra work and decreased accuracy.
Fortunately, in SAMSON, you can selectively minimize only a portion of a molecule by freezing the rest. This is especially useful in workflows like ligand fitting, loop refinement, or correcting localized geometry issues. In this post, we’ll walk you through how to perform partial minimization using SAMSON’s interactive minimizer and atom freezing capabilities.
When to Freeze Atoms
Atom freezing is a simple but powerful way of excluding specific atoms from being moved by the minimizer. Frozen atoms are completely fixed in space and do not respond during the minimization process. This allows you to isolate and refine a region of the molecule — such as a side chain, local loop, or solvent molecule — without affecting the rest of the structure.
How to Minimize Only a Portion of a Molecule
Here’s how you can refine a local region of a molecule using freezing in SAMSON:
- Select the entire molecule, or leave the selection empty to apply freezing to the whole document.
- Click Edit > Freeze. This will freeze all atoms in the selection (or the entire document if nothing is selected).
- Select the subset of atoms that you want to minimize (e.g., a flexible loop or interaction site).
- Click Edit > Unfreeze to make only these selected atoms mobile.
- Click Edit > Minimize to start interactive minimization. Use shortcut Z to toggle minimization on and off.
- When finished, click Edit > Minimize again to stop minimization.
- To allow editing the whole molecule again, click Edit > Unfreeze with all or no atoms selected.
This workflow is ideal when you want to refine a structural detail without affecting the coordinates of an established framework. It’s particularly effective for molecular design, constrained geometry optimization, and preparing systems for further simulation or docking.
Visual Feedback
To help you identify which atoms are frozen, SAMSON displays frozen atoms with a dark blue overlay in the viewport. This gives immediate visual confirmation as you work through the structure.
Useful Tip
Don’t forget that freezing is stateful across minimization operations. This means you can freeze or unfreeze atoms incrementally, providing complete control over which parts of the structure are affected during refinement.
To learn more about different minimization strategies in SAMSON, including system-wide minimization and use of simulators, refer to the full minimization documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.