A dense molecular structure can be difficult to explain one atom at a time. Simply turning off visibility may remove too much at once, while using transparency can leave a crowded image that is hard to read. When your goal is to guide an audience through a structure—showing what is present, then gradually clearing selected atoms from view—a staged concealment can make the change easier to follow.
In SAMSON, the Conceal atoms animation progressively hides selected atoms and the bonds between them. The key detail is that it changes node visibility, not transparency. So the selected atoms disappear from view rather than becoming translucent.
Plan the selection before animating
Start by choosing the atoms and bonds you want the animation to affect. Their order in the selection matters: during the progressive part of the animation, SAMSON hides atoms and the bonds between hidden atoms according to that order. If you want the disappearance to read as a clear progression, think about the order in which the selected atoms should vanish before you add the effect.
This is especially useful when preparing an explanation for a general audience. For example, you can use the sequence to move attention away from one part of a structure and toward what remains visible. The animation does not decide which atoms are scientifically most important; your selection and its order provide that direction.
What the four keyframes do
After selecting the atoms and bonds, double-click Conceal atoms in the Animation panel of the Animator. The effect has four keyframes, divided into three stages:
- Keyframes 1–2: the specified atoms and bonds are shown.
- Keyframes 2–3: selected atoms progressively disappear, with the sequence determined by their order in the selection. Bonds between hidden atoms are hidden as well.
- Keyframes 3–4: all specified atoms and bonds are hidden.
This structure gives you a visible starting state, a gradual transition, and a fully concealed end state. It can help avoid an abrupt cut when the purpose is to show a change unfolding rather than simply switch between two views.
Adjust the pacing to fit the explanation
You can move the animation’s keyframes to change when each stage occurs. If the audience needs more time to inspect the original structure, adjust the timing so the initial shown state lasts longer. If the progressive disappearance is the main point, give the middle stage more room. The exact placement depends on the pacing of your presentation; the important thing is that the keyframes are movable.
You can also change how parameters are interpolated between frames by modifying the easing curve. This gives you a way to adjust the character of the transition without changing which atoms were selected. Preview the result and check that the order of disappearance supports the point you are making.
A quick review before presenting
- Confirm that the intended atoms and bonds are selected.
- Check the selection order, because it determines the progressive hiding sequence.
- Review all three stages: shown, progressively concealed, and hidden.
- Move keyframes and adjust the easing curve if the transition needs different pacing.
Used this way, Conceal atoms is more than an on/off visibility change: it lets you control how a selected part of a molecular model leaves the audience’s view. For setup details and examples, see the Conceal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.