Freezing and Minimizing Parts of Molecules in SAMSON

One of the common challenges molecular modelers face is the need to optimize specific parts of a molecule without altering the rest of its structure. Whether you’re fine-tuning a specific region of a complex biomolecule or isolating changes to a single functional group, selective minimization is an essential capability. In SAMSON, you can achieve this with ease using the freeze and minimize options.

Why minimize a part of a molecule?

Molecules are often interconnected, meaning that changes in one section can propagate to others during optimization. This interconnectedness can lead to undesired changes outside your area of interest. By freezing parts of a molecule, you can keep them fixed while focusing the optimization on specific regions. This way, you retain control and achieve targeted adjustments.

How to minimize parts of a molecule in SAMSON

SAMSON offers a straightforward workflow for partial minimization. Here’s how you can do it:

  1. Select the molecule or keep the selection empty: Begin by selecting the entire molecule you’re working on or leave the selection empty if you want to apply changes to the whole molecule by default.
  2. Freeze parts you want to remain unminimized: Go to Edit > Freeze. This will ‘lock’ the positions of atoms in your selection or the entire system (if no selection is made). Frozen atoms will appear with a dark blue overlay in the viewport, clearly highlighting the parts that are fixed.
  3. Select the region to be minimized: After freezing, select the specific part of the molecule you wish to minimize. This could be a functional group, a side chain in a protein, or any other region of interest.
  4. Unfreeze the region to optimize: Use Edit > Unfreeze to unlock only the atoms in your current selection. This prepares the selected region for interactive minimization.
  5. Minimize the structure: Start the interactive minimization by choosing Edit > Minimize. During the minimization, you can observe the chosen region adjusting to its optimized geometry while the frozen areas remain fixed.
  6. Stop minimization: Click Edit > Minimize again to halt the minimization process when done.
  7. Unfreeze the full system: Once satisfied with your edits, make the entire structure movable again by clicking Edit > Unfreeze after selecting the molecule or leaving the selection empty.

The frozen atoms remain fixed in their positions and are excluded from optimization. This ability to isolate specific regions for minimization grants molecular modelers enormous control and flexibility.

Viewing frozen atoms

To help you visualize your workflow, SAMSON overlays frozen atoms with a dark blue color in the viewport, offering a clear indication of which parts of the molecule are fixed. This feature makes it easy to confirm your selections before proceeding with minimization.

Example in action

SAMSON also provides a helpful video tutorial demonstrating this workflow. By watching it, you can see a practical example of targeted minimization using frozen atoms:

Learn more

The freeze-and-minimize workflow is an essential tool for selective optimization, enabling precise molecular modeling. For complete details and more advanced workflows, visit the original documentation page at https://documentation.samson-connect.net/users/latest/minimizing/.

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

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