When building a molecular animation, it is easy to lose the thread of a sequence: a ligand, residue, or other node stays visible after it has stopped being relevant. Making it transparent may seem like the obvious fix, but transparency and visibility are different. A transparent object can remain faintly present on screen; the Hidden animation changes node visibility instead.
This distinction is useful when you want a clean transition between stages of an explanation—for example, when one set of nodes should no longer be shown before the next part of a presentation. Hidden is designed to make selected nodes hidden between two keyframes, giving you a way to control when they leave the view.
Set up the visibility change
- Select the nodes. Choose the nodes you want to hide. Being deliberate about the selection helps avoid hiding other parts of the molecular scene that you still need to show.
- Add the effect. In the Animator, open the Animation panel and double-click the Hidden animation effect.
- Position the keyframes. The begin keyframe is placed at the current frame. Move the animation’s keyframes as needed so the visibility change fits the timing of your presentation.
A practical way to plan this is to decide first what the audience should see at each stage. Then place the playhead at the intended starting point before adding the animation, and adjust the keyframes to match the sequence. Play back the animation and check whether the selected nodes disappear at the moment that makes the explanation easiest to follow. If the timing feels off, the keyframes can be moved; you do not have to rebuild the effect just to adjust its position.
Choose the right kind of change
Hidden is a good fit when the goal is for nodes to be out of view during part of the animation. It is not a transparency effect: the documentation specifies that it works through node visibility rather than transparency. If your intended visual result is a gradual fade, look at the related Disappear animation instead. For other visibility-related options, the documentation also lists Shown, Appear, Show, and Hide. Choosing an effect based on the visual change you actually need can make an animation clearer and avoid an unintended half-visible result.
Refine the timing
If the motion or parameter change between frames does not feel right, SAMSON lets you adjust how parameters are interpolated by changing the animation’s easing curve. For a straightforward hide/show sequence, first get the keyframe positions right; then explore easing if the transition’s timing needs refinement.
One interface detail to keep in mind: the documentation’s example movie uses an Animation menu that is no longer present in SAMSON. Animations are accessed through the Animation panel in the Animator, and presentation actions are available through the Animator’s controls.
For the exact steps and the related animation options, see the Hidden animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.