How to Minimize Only Part of a Molecule Without Affecting the Rest

When fine-tuning molecular structures, one common challenge is minimizing only a subset of atoms without disturbing the rest of the system. This might be needed, for example, when adjusting a flexible loop in a protein or fixing a local geometry, while keeping the surrounding molecular structure intact. Fortunately, SAMSON offers an efficient and intuitive way to perform partial minimization using freeze and unfreeze tools.

Instead of minimizing the entire molecular system, you can isolate and optimize only the region of interest. This functionality is available through SAMSON’s interactive minimizer, and here’s how to do it step by step.

📌 Step-by-step guide: Minimizing part of a molecule

  1. Select the entire molecule (or keep the selection empty if you want to freeze everything).
  2. Click Edit > Freeze to fix the positions of the selected atoms. If the selection is empty, all atoms in the document become frozen.
  3. Select the region of the molecule you want to minimize.
  4. Click Edit > Unfreeze to allow movement of only the selected atoms.
  5. Initiate the minimization with Edit > Minimize. This will optimize only the unfrozen atoms while keeping the rest fixed.
  6. Once satisfied, click Edit > Minimize again to stop the process.
  7. You can unfreeze the full molecule by selecting it (or leaving the selection empty) and clicking Edit > Unfreeze.

This approach is particularly useful for local refinement after a structural modification. You avoid unnecessary distortion of other parts of your molecule, ensuring that your modeling remains targeted and efficient.

🔵 Visual feedback: Frozen atoms

In the SAMSON viewport, atoms that are frozen are overlaid with a dark blue tint. This visual cue helps distinguish which parts of the molecule are fixed and which are active during minimization. It’s a simple yet effective way to keep track of selected regions as you work across complex models.

The interactive minimization preferences

If you’re curious to see this in action, here’s a video demonstrating partial minimization using frozen atoms:

Why use this feature?

This method is especially handy when working on large molecular systems. Instead of re-optimizing everything, which can be computationally expensive and possibly alter global geometry, focus only on what really needs to be adjusted. It’s fast, precise, and gives you more control over your modeling workflow.

Whether you’re cleaning up a localized geometry distortion or adjusting a residue after a mutation, partial minimization will become one of your go-to tools in SAMSON.

To learn more about different minimization options in SAMSON, visit the full documentation 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.

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