When working with complex molecular systems, full structural minimization can be overkill. Sometimes, modeling efforts focus on just one region of a molecule: the active site, a flexible loop, or a region that just underwent manual editing. In such situations, it’s helpful to minimize only a part of a molecule without disturbing the rest of the structure. SAMSON makes this surprisingly simple.
This blog post walks you through how to freeze parts of your molecule so that only your region of interest is minimized interactively. This technique is especially useful after adding or moving atoms, preparing a molecular system for simulation, or investigating local conformational changes, all without unintended global changes.
Why freeze before you minimize?
When you run a structural minimization in SAMSON using the Edit > Minimize command, by default the entire connected component (e.g., the whole molecule) gets optimized. If you only need to adjust a specific region, the rest of the molecule might still change during the minimization, which could introduce undesired deformations or require rework.
The solution is to freeze the rest of the molecule while keeping your target atoms unfrozen. Frozen atoms stay fixed during interactive minimization, ensuring localized optimization.
Step-by-step: Minimizing a selected part of a molecule
- Optionally select the entire molecule or leave the selection empty if you want to freeze everything in your document.
- Click Edit > Freeze. This will freeze either the selected atoms or the entire document if nothing is selected.
- Select the part of the molecule you’d like to minimize.
- Click Edit > Unfreeze to make only your selected atoms movable again.
- Now, click Edit > Minimize (or press
Z) to start the local minimization. - Once you’re satisfied with the result, click Edit > Minimize again to stop the process.
- Finally, unfreeze your system using Edit > Unfreeze if you want to continue editing normally.
Visual feedback and considerations
Frozen atoms are easy to spot—they appear with a dark blue overlay in the viewport. This visual cue helps keep track of which parts of the system are constrained, making your editing process more intuitive.
This method ensures other parts of your model stay untouched, which is especially helpful when working on local refinements or maintaining specific geometry elsewhere in the molecule. Just remember that if you select only part of a molecule without freezing the rest, SAMSON will still minimize the entire connected component that includes your selection.
Example in action
Want to see how this works? Here’s a short video illustrating the process:
To learn more about minimizing in SAMSON, including how to minimize full structures or use simulators, see the full documentation page: Minimizing in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.