In molecular modeling and animation, we often focus on what moves. However, sometimes what doesn’t move is just as important. For molecular modelers who want to control which parts of a molecule are in motion and which remain static, SAMSON offers a clear and effective solution: the Hold atoms animation effect.
Whether you’re emphasizing a binding site’s stability, highlighting a molecular fragment while others shift, or anchoring part of a molecule during a simulation, being able to fix certain atoms between two frames can be a game-changer for your presentations.
Why ‘Holding Atoms’ Matters
Creating scientific animations often involves guiding the viewer’s attention to a specific dynamic process — like ligand docking or a conformational change. But if everything in the scene moves, the viewer might lose context. That’s where holding atoms comes in.
The Hold atoms animation allows you to lock the position of selected atoms between two keyframes. The rest of the system can continue moving, changing, and transforming, but those selected atoms will stay in place, serving as a frame of reference or simply emphasizing structural stability.
How It Works
- Select the atoms or particles you want to remain still. You can do this using the standard selection tools in SAMSON. For example, you might choose a part of a protein backbone or a ligand.
- Open the Animator and locate the Animation panel. Double-click the Hold atoms effect.
- This will create a keyframe pair: between these frames, the selected atoms will be held static in space, even as the rest of the scene evolves.
- You can adjust these keyframes freely, changing the duration or position within the timeline.
The process is intuitive, but powerful. Combined with other effects—like Move atoms—you can create precise, informative animations that illustrate molecular mechanisms more clearly.
Example in Action
Take a look at the gif below. It combines the Move atoms and Hold atoms animations to show how part of a system can shift while another remains anchored. This kind of focus helps presentations become easier to follow and more scientifically meaningful.
Use Cases
Here are a few situations where the ‘Hold atoms’ animation can help:
- Fix a receptor while illustrating how different ligands approach it during docking.
- Show rigid fragments of a complex molecule while visualizing flexible linkers.
- Emphasize structural constraints by comparing free and restrained sections.
The Hold atoms feature is also used in various real presentations shared by the SAMSON community on SAMSON Connect, for example:
To learn more, visit the Hold atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.