Selective Minimization with Frozen Atoms in SAMSON

Molecular modeling often requires precision and flexibility when working with complex structures. A common challenge many molecular modelers face is how to refine only specific parts of a molecule while leaving others untouched. When adjustments are needed for localized regions of a structure, minimizing only those areas can save computational resources and prevent unintended structural changes to the rest of the molecule.

Fortunately, SAMSON provides a powerful and interactive way to handle such scenarios: you can freeze atoms to isolate parts of your molecule for minimization. Here’s a step-by-step guide to help you take advantage of this efficient workflow:

How Freezing Atoms Works

Freezing atoms allows you to fix certain parts of your molecular structure during minimization. These frozen atoms remain in their original positions, while unfrozen atoms are adjusted to achieve optimal geometry. This technique is particularly useful when working on localized modifications or when maintaining a specific conformation for parts of the molecule is crucial.

Step-by-Step Process

  1. Select the whole molecule or keep the selection empty to freeze the entire structure.
  2. Go to Edit > Freeze to fix the selected atoms in their current positions. If no selection is made, SAMSON freezes all atoms in the document.
  3. Select the specific part of the molecule you wish to minimize.
  4. Click Edit > Unfreeze to unfreeze only the selected atoms. This step ensures that only your chosen region is adjustable during the minimization process.
  5. Start the minimization by selecting Edit > Minimize. You’ll be able to interactively refine the geometry of the unfrozen section while the frozen atoms remain fixed.
  6. Once the minimization is complete, stop the process by clicking Edit > Minimize again.
  7. If necessary, unfreeze the entire molecule by selecting it and clicking Edit > Unfreeze. Alternatively, leave the selection empty and use the same option to unfreeze all atoms in the document.

Key Takeaways

  • Frozen atoms are displayed with a dark blue overlay in the viewport, making it easy to identify them during the workflow.
  • This approach is particularly useful for minimizing specific molecular regions while preserving the structural integrity of the rest of the molecule.
  • By freezing and unfreezing, you can achieve a balance between localized optimization and preserving important structural features.

The interactive minimization preferences

Visual Example

For an example of how freezing atoms enhances control in molecular minimization, watch the video below. It demonstrates the process clearly and highlights how frozen atoms remain fixed during minimization:

Feel free to experiment with this feature to see how freezing atoms can improve your molecular design workflow. To learn more about interactive minimization and related features, visit the SAMSON official documentation at this link.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from samson-connect.net.

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