When working on complex molecular systems, sometimes you need to refine only a specific part of a molecule—perhaps a side chain in a protein or a distorted fragment—without altering the rest of the structure. Fully minimizing the entire system can unintentionally move regions you want to leave untouched. Fortunately, SAMSON, the integrative platform for molecular design, lets you freeze specific atoms for partial minimization.
This post walks you through how to freeze parts of your molecular system to focus the minimization only where it matters. This technique is especially useful when adjusting regions after modifications or focusing on local energy refinements in large biomolecular structures.
Why freeze atoms?
Freezing atoms means telling the minimizer: “Leave these atoms alone.” This is essential when:
- You want to optimize only a mutated residue in a protein.
- You are modeling a ligand binding pose and want the target to stay fixed.
- Your structure is already in a good global shape but you need to fix a small distorted region.
How to minimize only part of a molecule in SAMSON
Here’s a step-by-step guide to minimizing parts of molecules using freezing:
- Select the whole molecule (or nothing at all).
- Click Edit > Freeze to freeze the selection. If no selection is made, the entire system is frozen.
- Select only the atoms you want to move and minimize.
- Click Edit > Unfreeze to allow movement only in your new selection.
- Begin the interactive minimization by clicking Edit > Minimize (shortcut: Z).
- Once the area is minimized to your satisfaction, click Edit > Minimize again to stop.
- To return everything to a normal editable state, click Edit > Unfreeze with the whole system selected (or with nothing selected).
Key Tip: Frozen atoms appear with a dark blue overlay in the viewport, so you can easily identify what will remain fixed during the process.
See it in action
If you’d like to watch how this process works in real time, here’s a short demo video from the documentation illustrating partial minimization with frozen atoms:
Wrapping up
Freezing atoms for partial minimization gives you greater control over structural refinements, making it easier to tune regions of interest without disrupting stable parts of your molecular system. Whether working on large polymers or small organic molecules, this practical feature can help streamline your modeling workflow.
For more details and additional options, see the full documentation page 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.