Keep the Right Atoms Still: A Simple Fix for Cleaner Molecular Animations

A molecular animation can become hard to follow when the viewer’s attention is meant to stay on one part of the structure, but that part keeps moving. Sometimes the clearest presentation is not to animate everything: hold a selected group of atoms in place for a defined interval while you arrange the rest of the sequence.

In SAMSON, the Hold atoms animation holds the positions of selected atoms between two frames. It gives you a straightforward way to keep a chosen group steady during part of a presentation—for example, when you want a viewer to focus on a change elsewhere in the scene.

Set up the interval deliberately

The effect applies to a group of particles that you select, and to the span between two keyframes. That makes two decisions important: which particles should stay fixed, and which section of the animation should they stay fixed for?

1. Select the particles. Choose the group whose positions you want to hold. Take a moment to check the selection before adding the effect: the selection determines what the animation will act on.
2. Add Hold atoms. In the Animator, open the Animation panel and double-click the Hold atoms animation effect.
3. Adjust the keyframes. Move the animation’s keyframes to set the interval during which the selected group is held at fixed positions.

The keyframes are not a one-time commitment. You can move them later, which is useful when the timing of a presentation changes or you want to refine how long the still interval lasts. Rather than rebuilding the animation, adjust the interval to fit the story you want the sequence to tell.

Make stillness part of the explanation

A held group can provide a visual reference point. If a sequence includes movement, a steady region may help viewers compare what changes against what remains in place. Before adding the effect, ask what the viewer needs to track. If the selected group is the subject of the movement, holding it may obscure the point; if it is useful context, keeping it steady may make the change easier to read.

It can also help to think of the animation in intervals. Identify where the viewer should see motion, where a pause would clarify the structure, and which particles belong in that pause. Then position the two keyframes around that interval. This simple planning step can make a presentation feel more intentional without adding extra visual complexity.

Find the animation controls

Some older demonstrations show an Animation menu. That menu is no longer present in SAMSON: access animations through the Animation panel in the Animator. The Animator’s controls are also where you can access presentation actions.

For examples of presentations using Hold atoms, the documentation lists 2AZ8 – Dock animation, 2XQ6 – Assemble animation, and 5SAT – Dock animation. To compare it with an animation intended to move atoms, see Move atoms.

For the full instructions, visit the Hold atoms documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.