Fixing Atoms Between Frames: A Simple Way to Clarify Molecular Motion

When creating molecular animations, clarity is key. Animations are often used to illustrate conformational changes, docking events, or assembly mechanisms—but what happens when the entire structure is moving, and you just want to highlight a specific interaction or motion?

Unwanted movement of atoms or molecules in a scene can reduce the interpretability of molecular animations. This is where holding atoms fixed between frames becomes useful. In SAMSON, the Hold atoms animation helps modelers freeze the position of specific atoms (or groups of atoms) during transitions, allowing clearer visualizations.

Why hold atoms in place?

Imagine simulating a ligand docking into a receptor. If both the receptor and the ligand move simultaneously, it becomes difficult to focus the visual narrative on the docking process. By holding the receptor atoms at fixed positions during specific time intervals, molecular designers can create much more comprehensible sequences.

How it works in SAMSON

The Hold atoms animation in SAMSON allows you to lock the position of selected atoms between two keyframes within the Animator. This animation is especially useful in presentations where relative motion (rather than absolute motion) is essential to the audience’s understanding.

Here’s a quick guide to using it:

  1. Select the group of atoms you want to hold still. You can do this using SAMSON’s selection tools. More on selecting atoms is here.
  2. Then, open the Animator (via Ctrl+7 or Cmd+7, based on your OS) and locate the Animation panel.
  3. Double-click on the Hold atoms effect.
  4. Adjust the keyframes to define the time interval during which the atoms should remain fixed.

That’s it. You’re now holding atoms steady in time, making your animation easier to interpret.

When to use this technique

  • Docking animations: Hold the receptor in place while showing the ligand approaching.
  • Protein conformational changes: Lock part of a protein (e.g., the core) to emphasize the movement of a loop or domain.
  • Assembly animations: Keep already assembled components steady as new parts join.

Here’s an example using both Move atoms and Hold atoms effects together:

Example: the Move and Hold atoms animations

Additional tips

  • You can freely move the keyframes where the hold begins or ends—great for fine-tuning.
  • The Hold atoms animation is additive, so you can use it alongside other effects (like move, rotate, or fade) to build more complex narratives.
  • Make use of previous examples from SAMSON Connect’s Documents hub for inspiration. For instance, check out the Assemble animation demonstrating this approach.

Whether you’re preparing a presentation, publishing visual material, or simply gaining insight into a simulation outcome, the ability to hold specific atoms steady can make a big difference.

You can learn more about this feature and see additional examples on the Hold atoms documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.

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