Locking Molecular Positions: Why and How to Hold Atoms in Animations

In molecular modeling, creating compelling and instructive animations often means clearly highlighting key interactions or transformations—without distracting motion in other areas. Ever tried to animate a docking event only to find unrelated atoms drifting around, distorting the focus of your presentation?🎯 That’s where the Hold atoms animation effect in SAMSON comes in.

Prevent unwanted movement in your molecular animations

Animations are a great way to convey molecular mechanisms, conformational changes, or binding events. However, uncontrolled motion (often due to interpolation between keyframes) can lead to distracting visuals. Sometimes, a ligand is supposed to move into a pocket while the protein remains static — but you find parts of the protein subtly shifting. This is not only distracting, it can also mislead your audience.

The Hold atoms animation effect provides a targeted solution: it lets you freeze the position of selected atoms between two frames, keeping them steady while everything else can animate freely.

How to use Hold atoms in SAMSON

  1. Select the group of particles you want to keep fixed—for example, the backbone of a protein while the side chain or a ligand moves.
  2. Open the Animation panel via the Animator.
  3. Double-click on the Hold atoms animation effect to apply it to the selected atoms.
  4. Adjust the keyframes to indicate the range where atoms will be held fixed. You can always modify the keyframe positions later.

The result: atoms in your selected group will not interpolate between frames. Instead, they stay locked in place, maintaining clarity and focus in your animation.

When is this useful?

Here are three situations where Hold atoms can significantly improve your animation quality:

  • Docking animations: Make the incoming ligand the star of the show by stabilizing all protein atoms.
  • Mutation simulations: Lock non-mutated atoms in place to emphasize the differences.
  • Step-by-step mechanisms: Animate molecular reorganization in logical steps, freezing parts of the system when needed.

Example: the Move and Hold atoms animations

Try it out

Want to see it in action? Explore examples that use this technique on SAMSON Connect, such as:

For more details and step-by-step guidance, visit the official Hold atoms documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. Download the platform from www.samson-connect.net.

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