How to Minimize Just Part of a Molecule in SAMSON Without Affecting the Rest

When working with complex molecular systems, you sometimes need to optimize just a portion of a molecule—such as a side chain, a loop, or a binding site—without disturbing the rest of the structure. Minimizing the entire molecule can lead to undesired modifications, especially if you’re refining a local region after manual edits or preparing a structure for simulation. Fortunately, SAMSON offers a practical solution through partial minimization with frozen atoms!

In this post, we’ll explore how you can use SAMSON’s interactive minimization editor to minimize only specific parts of a molecule while keeping the rest fixed. This technique is especially useful for:

  • Preserving global conformation while adjusting local areas
  • Preprocessing molecular models for docking or simulation
  • Fixing local geometry errors after fragment replacement or editing

Step-by-step: Freezing and Minimizing in SAMSON

To minimize just a part of a molecule in SAMSON, you need to selectively freeze the atoms you don’t want to move. The remaining unfrozen part will then be optimized using the Universal Force Field (UFF). Here’s how you do it:

  1. Select and freeze:
    1. Select the entire molecule, or leave the selection empty to target the whole document.
    2. Go to Edit > Freeze. This locks all atoms in place.
  2. Unfreeze your region of interest:
    1. Select the part of the molecule you wish to minimize (e.g., a side chain).
    2. Click Edit > Unfreeze. Only the selected atoms will now be movable during minimization.
  3. Minimize interactively:
    1. Click Edit > Minimize. SAMSON will optimize only the unfrozen atoms using the UFF.
    2. Click Edit > Minimize again to stop.
  4. Unfreeze everything:
    When done, unfreeze the full system by selecting the molecule (or nothing) and clicking Edit > Unfreeze.

Visibility Tips

You’ll easily recognize frozen atoms—they appear with a dark blue overlay in the viewport. This visual cue helps you avoid accidental manipulation during selective minimizations.

Why Partial Minimization Can Help You

Partial minimization is a practical feature when you’re performing local model corrections or building models incrementally. For example, if you’re modifying the binding site of a protein and only want to test a new conformation of a ligand without moving the rest of the structure, freezing the backbone and minimizing only the new group prevents unintended distortions elsewhere in the molecule.

Below is an example video demonstrating partial minimization using frozen atoms:

Adjusting Preferences

You can tune the behavior of the minimizer in Interface > Preferences > Editors > Minimize. By default, SAMSON minimizes all atoms in the document. To work with selections only, make sure to uncheck the Include all atoms in the document option:

The interactive minimization preferences

For additional scenarios such as minimizing a full molecule or using simulators with different force fields, see the complete SAMSON minimization guide at this documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.

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