When working with molecular animations, one common challenge is keeping part of a system still while another part moves. You might want to show a ligand docking into a receptor and keep the receptor rigid, or illustrate the movement of one domain while anchoring another. This kind of selective motion control is essential for clarity and scientific communication.
In SAMSON, you can solve this problem using the Hold atoms animation. This feature allows you to lock the position of specific atoms between two animation frames, ensuring that these atoms remain perfectly still while others may move or transform around them.
What does “Hold atoms” do?
The Hold atoms animation freezes the selected atoms’ positions between two keyframes in your storyboard. This means that once you’ve selected a group of atoms and added a ‘Hold atoms’ effect to them, they won’t drift, rotate, or transform during that interval.
This is particularly useful in the following scenarios:
- Fixing a receptor while a ligand moves during a docking simulation.
- Holding one domain of a protein to highlight the motion of another domain.
- Creating didactic animations by isolating distinct molecular events in time.
How to use the “Hold atoms” animation
- Select the atoms or group of atoms you want to hold fixed. This can be done using SAMSON’s selection tools.
- In the Animation panel (available via the Animator interface), double-click on the Hold atoms effect.
- Adjust the keyframes on the timeline to define the duration during which the atoms should remain fixed.
SAMSON allows full control over these keyframes, so you can easily reposition them as your animation evolves. This flexibility keeps your storytelling smooth and precise.
In the animation above, one group of atoms is held fixed while another moves, highlighting just how useful this method can be for cleanup and clarity.
A few tips
- If you’re not seeing the animation panel, you can open it via
Animator (Ctrl+7 or Cmd+7). - This effect is independent of the model’s original state—it’s purely visual; it affects the presentation, not the simulation results.
- You can combine Hold atoms with other effects like Move atoms for more complex animations.
Example use cases
You can explore and share examples of this technique in action on SAMSON Connect:
Learn more in the full documentation for Hold atoms animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at www.samson-connect.net.