When working on molecular animations, it’s common to encounter a challenge: how do you isolate the motion of certain atoms or groups while keeping others perfectly still? Whether you’re preparing a presentation to highlight a binding site mechanism or illustrating a chemical reaction pathway, having complete control over what moves—and what doesn’t—can make or break your animation clarity.
This is where the Hold atoms animation in SAMSON comes in. It solves a specific problem faced by many molecular modelers: the need to keep a group of atoms fixed during part—or all—of an animation without affecting their environment or requiring additional software scripting. Holding atoms steady can help you highlight crucial dynamics, especially in cases like:
- Ligand movement toward a static receptor site
- Protein domain motions with fixed anchor points
- Component assembly animations where certain subunits should remain stationary
How it works
Using Hold atoms in SAMSON is simple and doesn’t require presets or manual keyframe manipulations. Here’s how to use it:
- Select the atoms or particles you want to keep fixed using the standard selection tools. This selection could span atoms across multiple residues or even different molecular components.
- Open the Animator by going to Interface > Animator, or use the shortcut Ctrl + 7 (on macOS: Cmd + 7).
- In the Animation panel, double-click on Hold atoms to insert the effect between two keyframes. The selected atoms will remain at their positions between those frames.
To refine your animation:
- Drag the keyframes to extend or shorten the hold duration.
- Combine Hold atoms with other effects, like Move atoms, to create more complex sequences and interactions between dynamic and static parts of your model.
Above is an animation created using both the Move atoms and Hold atoms effects. Notice how some atoms shift position while others stay perfectly still—ideal for highlighting specific motions without distracting the viewer.
What to keep in mind
The Hold atoms feature doesn’t permanently alter atom positions—it just freezes their animation between keyframes. You can still apply transformations before or after the hold effect, giving you fine-grained control over your animation timeline. Plus, you can always revisit and move the keyframes if needed.
Want to see it in action?
Examples of documents using the Hold atoms animation are available directly on SAMSON Connect:
To learn more about the Hold atoms animation, visit the original documentation page: https://documentation.samson-connect.net/users/latest/animations/hold-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.