Exploring complex molecular transformations often means working with trajectories that capture conformational changes or dynamic processes. One of the common challenges molecular modelers face is presenting those trajectories in an intuitive and synchronized way — especially when paths don’t align in length or need to cycle between conformations.
If you’re a SAMSON user, there’s a helpful feature that directly addresses this: the Play path animation effect. This tool lets you animate one or more paths smoothly between two timeline frames on the animation panel. This is particularly effective for visualizing simulations, reaction pathways, or simply creating clear presentation materials.
What Is a Path in SAMSON?
In SAMSON, a path node stores a trajectory—a sequence of conformations or positions over time. This could come, for instance, from a molecular dynamics simulation or manually defined conformations between key states. The Play path effect utilizes these to create compelling animations directly on the Animator timeline.
Setting Up a Play Path Animation
Here’s how you can animate molecular transformations using the Play path effect:
- First, make sure you’ve selected the path node you’d like to animate.
- Then, in the Animation panel, double-click on the Play path effect. This will insert the animation between two default keyframes.
- Adjust the keyframes to control how long the animation lasts in your scene. This gives you temporal control on how the trajectory unfolds.
Even more useful, if you select multiple paths before applying the effect, they will all be synchronized in the animation. This makes it easy to compare molecular systems evolving in parallel (for example, comparing two runs of molecular dynamics or analyzing alternative reaction routes).
Smoothing and Interpolation
Sometimes, the number of frames in the animation may not match the number of frames in your trajectory. SAMSON handles this by smoothing the trajectory automatically — interpolating between conformations to fill the time gap. If you want to visualize discrete, original steps only, you can disable smoothing from the Inspector.
Additionally, for those interested in pacing, SAMSON enables fine-tuning how motion varies over time through the Easing curve. Adjusting this lets you choose between easing in, easing out, or linear movement — giving you presentation-level control over the animation dynamics.
Tip: Always Move Keyframes
One of the flexible features of SAMSON is that you can reposition animation keyframes at any time. So, after seeing the initial motion preview, feel free to tweak keyframe placement along the timeline to match desired timing and effect.
A Simple Way to Improve Visual Communication
For educators, researchers, and students alike, visualizing how molecules change over time can be just as important as the data itself. The Play path animation makes this easier, without requiring scripting or external software. Whether you’re preparing a lecture or clarifying a mechanism in a publication draft, it’s a neat feature worth exploring.
To learn more, visit the full documentation on the Play path animation effect.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.