In many molecular simulations and visualizations, it can be helpful to highlight or isolate the behavior of part of a system while keeping another part immobile. For example, you might want to animate a ligand entering a binding pocket while the receptor remains still. Or you may wish to demonstrate the relative motion of one domain of a protein while the other stays fixed for clarity.
This is a common visualization challenge: how do you make only some parts of a molecular system move between animation frames, while others remain perfectly still? Luckily, SAMSON has an animation effect specifically for this: Hold atoms.
Why hold atoms?
In molecular model building and presentations, animations are often used to tell stories: how a ligand docks, how a protein folds, or how a complex dissociates. But when everything moves at once, it can become confusing for viewers to interpret what’s actually changing. Holding some atoms fixed allows viewers to focus on what’s important.
For example:
- Hold the receptor fixed while the ligand docks.
- Freeze part of a complex to emphasize the motion of another part.
- Restore a local section of the molecular system to a reference frame.
How to freeze parts of your system
To use the Hold atoms animation in SAMSON:
- Select the atoms you want to keep fixed between two frames. You can do this through the selection tools explained in the selection documentation.
- Open the Animator, and in the Animation panel, double-click on Hold atoms.
- This creates an animation effect that holds the selected atoms in place between two keyframes. You can adjust the keyframes as needed to define the range of frames during which the atoms stay fixed.
If you’re combining Hold atoms with other effects like Move atoms, you can get interesting presentations where some parts of the system remain anchored while others transition smoothly between configurations.
Examples you can explore
Here are a few example documents on SAMSON Connect that make use of the Hold atoms animation:
These examples show how combining animation effects makes it easier to convey molecular mechanisms clearly, even in complex systems.
What to keep in mind
Note that you can always reposition the keyframes after you’ve added the animation. This gives you the flexibility to precisely control when and for how long atoms remain fixed. Also, please be aware that the animation menus have evolved: access to animation effects is now done through the Animation panel in the Animator, not through previous versions’ menus.
To learn more, visit the full documentation page on the Hold atoms animation effect.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.