When preparing molecular animations, one common challenge faced by modelers is selectively immobilizing parts of a structure while letting others move. For example, you might want to show a ligand docking into a protein but keep the receptor rigid throughout the animation. This is where the Hold atoms animation effect in SAMSON becomes a valuable tool.
Instead of manually repositioning components frame by frame or relying on complex scripting, the Hold atoms effect provides a straightforward way to preserve atomic positions between two keyframes. Whether you’re demonstrating binding, docking, folding, or assembly, using this effect helps isolate motion and draw attention to key molecular movements, while maintaining clarity in your presentation.
What does “holding atoms” mean?
In an animation, objects typically interpolate between different positions over time. However, sometimes you want certain parts to stay fixed, even while the animation progresses. The Hold atoms animation freezes the selected particles, keeping their positions locked between two specified keyframes. Outside of this interval, the atoms can still move freely.
How to use the Hold atoms effect
- Select the atoms or group of particles you want to keep fixed. Use the standard selection methods in SAMSON (see Selecting guide).
- Open the Animation panel of the Animator. You can do this with the keyboard shortcut
Ctrl+7(orCmd+7on macOS). - Double-click on the Hold atoms effect to add it. A new animation track will appear.
- Adjust the keyframes of the Hold atoms effect to cover the timeframe where you want atom positions locked.
That’s it! The selected atoms will remain exactly where they are during the interval between the chosen keyframes. You can still move the keyframes later to fine-tune the effect.
Use cases that benefit from holding atoms
- Docking animations: Keep the receptor structure still while showing a flexible ligand moving into the binding pocket.
- Assembly processes: Show subunits assembling into a complex around a fixed core.
- Folding sequences: Anchor residues or regions that have already formed stable structures.
The image below illustrates how this can be used in combination with movement — part of the molecule moves, while the rest is held in place:
Where to find examples
You can explore ready-made SAMSON documents using this technique on SAMSON Connect, such as:
These examples showcase how combining Hold atoms with motion effects can effectively communicate biological mechanisms or structural changes.
To learn more about the Hold atoms effect and animation workflows, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/hold-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.