Molecular animations are more than just eye candy—they’re essential for communicating structural transitions, mechanisms, and design ideas. But what happens when certain parts of a model clutter your scene or distract from the key mechanism you’re trying to convey?
Whether you’re preparing a presentation or sharing a molecular mechanism with collaborators, there will be moments when you want to hide parts of your model, temporarily and precisely. That’s where the Hidden animation in SAMSON comes in.
What does the Hidden animation do?
The Hidden animation makes selected nodes completely invisible between two keyframes. This differs from transparency effects: the nodes become non-visible, which can help reduce visual noise when focusing on a specific region of a molecular assembly.
This is particularly useful when tracing conformational changes, isolating molecular interactions, or producing clean scenes for visual storytelling. Gone (but not forgotten!) components reappear at the end of the animation interval as you configure it.
How to apply the Hidden animation
Here is a straightforward workflow to apply the animation:
- Select the nodes you want to hide. These could be side chains, residues, solvent molecules, or even entire domains.
- In the Animation panel of the Animator, double-click on the Hidden effect.
- This sets the beginning keyframe at the current frame—nodes start becoming hidden.
- Adjust the keyframes to control when the nodes disappear and when they reappear.
Above: both the Shown and Hidden animations in action demonstrate the dynamic control you have over visibility.
What makes this powerful
Because this is a hard visibility toggle (unlike fading or transparency), it is particularly clean in explanatory animations. For instance: want to show a substrate binding event, but the protein’s flexible loop is blocking the view? Use the Hidden animation to temporarily remove it at just the right time. Want to compare pre- and post-docking configurations? Hide everything except the ligand before revealing the receptor structure.
The transitions can also be made elegant with easing curves—these control the interpolation speed of the changes, helping you better pace your narrative.
Tips to keep in mind
- You can move and adjust keyframes even after applying the animation.
- The Animation menu shown in some older tutorials has been removed—now all effect controls are centralized in the Animation panel.
- Combine Hidden with other effects like Shown or Flash for advanced workflows.
For more details, see the documentation page: https://documentation.samson-connect.net/users/latest/animations/hidden/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.