When creating molecular animations, one challenge that frequently arises is the need to visually isolate motion. Suppose you’re showcasing how a drug docks into a protein’s binding site, and you want only the ligand to move — not the entire complex. This is a common situation where too much motion in the scene confuses viewers.
Enter the Hold atoms animation in SAMSON — a minimal yet practical tool that allows you to lock specific atoms or molecular fragments in place between animation keyframes, helping you keep your scene focused and clear.
Why you might need this
In complex biomolecular systems, even small changes can lead to overwhelming visual outputs when everything moves simultaneously. If you’ve ever tried to animate a docking or assembly process, chances are you’ve struggled to control the chaos.
By freezing the motion of non-interacting or background elements—like a receptor protein in a docking animation—you can direct your audience’s attention where it matters most.
How it works in SAMSON
The Hold atoms animation works by fixing the position of a selected group of atoms between two keyframes.
- Select the group of particles (atoms, residues, molecules) you want to keep still. This is easily done using SAMSON’s selection tools.
- Open the Animation panel in the Animator. Then double-click on the
Hold atomsanimation. - Two keyframes will be created, and the selected atoms will be held in fixed positions between them.
- Adjust the keyframes to set the duration of the frozen interval.
Combining with other effects
The real value of Hold atoms comes out when combined with other animations like Move atoms. For example, you can hold the receptor still while animating the approach of a ligand. The result? A cleaner, more digestible representation of the molecular interaction.
This GIF shows exactly how this works: while one part of the molecule is in motion, another remains stationary, improving clarity and visual impact.
Practical examples
To better grasp the possibilities, check out these real examples from the SAMSON Connect document library where Hold atoms plays a critical role:
If you’re interested in creating scientific presentations or educational materials that focus attention and reduce visual clutter, this technique might be well worth adding to your workflow.
To learn more about how the effect works and additional tips, visit the official documentation page: Hold atoms animation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.