In molecular modeling, clear communication is essential. Whether you’re presenting a mechanism to collaborators or preparing a visual for publication, controlling the visibility of molecules or molecular fragments at specific times can dramatically improve audience understanding.
This is where the Hidden animation in SAMSON can help. Unlike animations that gradually fade an object in or out using transparency, the Hidden animation works by switching the full visibility of nodes between two keyframes. The object is either visible or not—making this ideal for drawing attention to specific moments or structures in molecular processes.
Common Problem: Overloaded Visuals
When explaining complex interactions, too many visible elements can overwhelm your audience. You could use transparency to mitigate this, but that often only dims the confusion. A clearer solution is to completely hide distracting elements during certain parts of your animation.
Creating the Hidden Animation
Here’s how you can quickly implement the Hidden animation in SAMSON:
- Select the nodes you want to hide. These could be atoms, molecules, or even entire molecular assemblies.
- Double-click on the Hidden animation in the Animation panel of the Animator. This assigns the begin keyframe at the current time frame.
- Move forward in time to a later frame, and the object will be hidden by then. Keyframes can be adjusted freely to match your narrative timing.
This technique is helpful when you want an object to be visible early in an animation and become invisible to spotlight other events later.
Control the Style of Disappearance
Want to fine-tune how objects disappear? With SAMSON, you can use Easing curves to adjust the interpolation between frames. Even though the Hidden animation creates a binary visibility effect (on/off), easing curves can help coordinate the disappearance of multiple objects for synchronized storytelling.
See It in Action
The example below shows how the Shown and Hidden animations can be combined to create object reveal/hide sequences at different stages of a molecular animation:
Keep in Mind
- If you’ve used older versions of SAMSON, the Animation menu previously used in tutorials has been replaced by the Animation panel in the Animator. All presentation-related actions are now accessible via the Animator’s controls.
- You can always reposition keyframes after they’ve been created, providing flexibility as your visual narrative evolves.
Animations like this are not just cosmetic—they genuinely help viewers understand your models efficiently. Simple changes in visibility can clarify reaction centers, distinguish between molecules, or emphasize dynamic processes like docking or rearrangements.
Learn more about the Hidden animation in the SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.