If you’re modeling molecular systems with multiple molecules, you’ve probably encountered this issue: you want to fine-tune a single molecule or part of it without affecting the rest of your system. Maybe you’re adjusting a ligand conformation in a protein-ligand complex, or optimizing a single fragment in a multi-component design. Thankfully, interactive minimization in SAMSON gives you precise control over what gets minimized—and what stays fixed.
In SAMSON, the default minimization affects all molecules in the active document. This makes sense if you’re starting from scratch, but if you’re iteratively refining a system, being able to restrict minimization becomes essential.
Minimizing a Single Molecule Without Affecting Others
To minimize just one molecule (i.e., one connected component) in a multi-molecule project, follow these steps:
- Open Interface > Preferences > Editors > Minimize.
- Uncheck the option Include all atoms in the document.
- Select the molecule you want to minimize (learn about selection here).
- Click Edit > Minimize, or press Z on your keyboard.
This will run the interactive minimizer—but only on the molecule you selected. SAMSON automatically identifies and minimizes the entire connected component that includes your selection.
Note
If you select only a single atom, the full molecule connected to that atom will still be minimized. If you want to minimize just part of a molecule, read on.
Zoom In Further: Minimizing Only a Part of a Molecule
Sometimes you want to optimize just a fragment—say, a side chain or a flexible region—and keep the rest untouched. Here’s how to do it using SAMSON’s freeze/unfreeze mechanism:
- Select the whole molecule (or leave everything unselected).
- Click Edit > Freeze to freeze either the selection or the entire system.
- Select only the atoms you want to minimize.
- Click Edit > Unfreeze to unfreeze the editable region.
- Click Edit > Minimize to start interactive minimization.
- Once you’re done, click Edit > Minimize again to stop.
- To unfreeze everything, click Edit > Unfreeze again.
Frozen atoms remain fixed and are visualized with a dark blue overlay in the viewport.
When Should You Use This?
- Refining docking poses without disrupting the protein backbone
- Optimizing a faulty fragment geometry without re-minimizing the whole molecule
- Performing localized conformational tweaks in large systems
Here’s a quick look at the Preferences panel where you can disable full-document minimization:
This selective approach is especially useful when collaborating on large structures where various researchers work on different fragments. You can focus on your area without interfering with others’ modifications.
Interested in learning more detailed steps? Visit the interactive minimization guide.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.