Keeping Molecules Still for Better Animations

When working on molecular animations, one of the most common frustrations that molecular modelers face is keeping parts of a molecule steady while the rest of the system moves. Whether you’re showcasing ligand docking, domain movement, or assembling large biomolecular complexes, sometimes all you need is for a few atoms to just stay put. This may sound simple, but unless your animation tools support partial movement, it can involve tedious workarounds like editing multiple frames manually – a task not many enjoy.

Fortunately, SAMSON provides a focused and elegant solution: the Hold atoms animation.

Fixing Atoms Between Keyframes

The Hold atoms animation lets you select a group of particles and ensures they remain at fixed positions between two animation frames, even while the rest of the model continues to evolve dynamically.

This is especially useful when you want to:

  • Emphasize motion of a specific domain by keeping the rest static
  • Display docking animations where the receptor remains fixed
  • Simulate an environment where only a subset of atoms are mobile (e.g., flexible loop regions)

How to Use It

Using the Hold atoms animation is simple:

  1. Select the atoms you wish to fix. This is usually done via the selection tool.
  2. Open the Animator (accessible through Interface > Animator or by pressing Ctrl+7 on Windows/Linux or Cmd+7 on macOS).
  3. Double-click on the Hold atoms animation effect in the Animation panel.
  4. The selected atoms will now stay in place between the two nearest keyframes. You can move the keyframes as needed to control which time interval the atoms are held still.

You can always adjust the timing by dragging the keyframes directly. This makes it easy to try different effects without redoing the animation from scratch.

Example Visualization

Here’s an animation showing both Move atoms and Hold atoms in action. The selected group of atoms remains in place while another group translates through space, making it easier to understand which part of the system is undergoing change.

Example: the Move and Hold atoms animations

Whether you’re making an educational video or presenting your results, holding atoms still at key moments can improve clarity and focus.

More Examples

Here are a few real-world presentations created in SAMSON that use the Hold atoms animation:

Want to explore further? Visit the full documentation for the Hold atoms animation here.

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

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