When creating molecular animations for presentations or publication, many researchers face a challenge: how to isolate and clearly communicate the motion of a specific part of a molecule, such as a ligand docking into a protein binding site, when the rest of the system is also moving. Motion everywhere can blur the clarity of what matters most in a dynamic visualization.
This is where SAMSON’s Hold atoms animation can help. It allows you to keep the positions of selected atoms fixed between two animation keyframes. This feature is especially useful when the goal is to emphasize a local structural change or interaction—such as ligand binding, domain movement, or reorientation—without distraction from global molecular fluctuations.
Why fix atoms in molecular animations?
Let’s say you’re visualizing a docking simulation. The ligand moves into position and binds the protein—so far so good. But if surrounding residues or domains are subtly shifting due to thermal motion, it becomes harder for a viewer to immediately notice the essence of the conformational event. By fixing the protein (or even just its key residues) using Hold atoms, the viewer’s attention is drawn more directly to the movement of the ligand.
How to use ‘Hold atoms’ in SAMSON
The process is intuitive:
- Select the atoms you want to keep static between two frames.
- Open the Animation panel in the Animator.
- Double-click on Hold atoms in the animation effects list.
- Move the animation keyframes to define the time window in which the atoms should be held in place.
That’s it. The selected group will retain their position between the defined frames. Outside of this time range, they resume natural motion if present.
Best practices
Here are a few tips to make the most of this feature:
- Use it selectively. Fix only the atoms you need to keep stationary to guide visual attention without compromising the integrity of the motion.
- You can combine this with Move atoms to contrast motion between parts of the system—for example: hold the receptor, move the ligand.
A visual example
Below is an example of how Move atoms and Hold atoms can be used together to create a clearer visualization of interaction dynamics in a molecular model:
Explore real case studies
Examples of actual animations available via SAMSON Connect that utilize the hold atoms feature:
To learn more about this feature and start applying it in your own visualizations, visit the official documentation page: Hold atoms animation – SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.