If you’ve ever tried to animate a molecular system, you’ve probably faced this: you want to show certain parts of the molecule moving, while others remain still. But without a way to fix parts of the structure, animations can quickly become confusing. What actually moves—and what doesn’t—is hard to decipher visually.
This is a common issue in the visualization of docking, conformational changes, or protein–ligand interactions. When everything moves together, it’s difficult for your audience (and sometimes even yourself) to understand what’s flexible and what’s constant.
Fortunately, SAMSON provides a simple yet powerful animation effect: Hold atoms. This animation freezes the selected atoms in place between two frames, giving you precise control over how your structure is presented. It’s especially useful in combination with the Move Atoms feature—but it can also be effective on its own.
How It Works
You can apply the Hold atoms animation in just a couple of steps. First, select the group of atoms that should remain fixed. Then, in the Animation panel of the Animator, double-click the Hold atoms effect. SAMSON creates keyframes, and between these two, the selected atoms will stay put.
Want to fine-tune the timing? No problem. You can move the keyframes forward or backward to adjust when the atoms are held. This is especially useful if you’re synchronizing multiple animation effects.
When to Use ‘Hold Atoms’
- Protein-ligand docking: Keep the protein static to highlight how the ligand enters and binds.
- Multimer assembly: Fix one subunit while animating the others docking into place.
- Local conformational changes: Emphasize flexible loops or domains by fixing the rest of the structure.
Here’s an illustration combining hold and move animations to make a motion clear:
Tips
- Use different colors or styles to visually separate held and moving parts.
- Don’t forget that you can view and adjust all keyframes in the Animator panel—just go to Interface > Animator or press Ctrl + 7 (Cmd + 7 on Mac).
- Try using the ‘Hold atoms’ effect on solvent molecules when you only want to highlight solute behavior.
Examples To Explore
Check out these animations created using this effect:
By combining simplicity and precision, the ‘Hold atoms’ animation helps clarify molecular motion—a must for anyone needing to visually communicate how biomolecular systems behave.
Learn more about the ‘Hold atoms’ animation in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.