Interactive molecular minimization in SAMSON is convenient and fast, but what if you’re only interested in minimizing part of a molecule—say, just a few atoms or a flexible side chain—without altering the rest of the structure?
When setting up a large or complex system, full geometry optimization can sometimes be unnecessary, or even unwanted. You might want to keep parts of the system fixed (like metals, ligands, or structural scaffolds) while only locally relaxing specific atoms. This is especially important in workflows where you import parts of the system from experimental structures and only want to refine specific regions under your control.
In SAMSON, this is where Freezing becomes very useful.
How it works
SAMSON provides a way to exclude some atoms from geometry optimization during interactive minimization. By freezing all atoms initially and then unfreezing the ones you want to minimize, you gain precise control over what gets updated.
Step-by-step: Partial minimization using freeze/unfreeze
- Select the whole molecule or leave the selection empty if you want to freeze everything in the scene.
- Click Edit > Freeze. This will fix all selected atoms in space.
- Now select only the region you want to minimize (for example, a loop in a protein, a specific functional group, or a bound ligand).
- Click Edit > Unfreeze. Only these atoms will be allowed to move during minimization.
- Start minimization using Edit > Minimize or shortcut Z. When you’re done, click the same command or press Z again to stop.
- Finally, if desired, click Edit > Unfreeze with nothing selected to unfreeze the whole system.
Note: Frozen atoms appear with a dark blue overlay in the viewport, making it easy to verify which parts of your system are fixed.
Here is a visual overview from the documentation showing the Freeze/Unfreeze preferences and behaviors:
This technique is especially helpful when working with hybrid approaches where parts of the model come from experiment or other simulations, and you only want to optimize the newly modified or built regions.
Why this helps
Minimizing only a portion of a structure:
- Preserves trusted geometry (e.g., crystallographic positions).
- Saves time during interactive editing.
- Reduces unintended structural drift in sensitive regions.
- Makes editing and refinement much more controlled.
It’s worth noting that even if you select just one atom, SAMSON automatically includes all atoms connected to it via covalent bonds. This ensures chemical integrity during minimization. To go beyond that, use Freeze/Unfreeze to manually define your minimization scope.
📺 Prefer seeing it in action? Check out this short video from the documentation showing minimization with frozen atoms in action:
To learn more, visit the official documentation: https://documentation.samson-connect.net/users/latest/minimizing/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.