When working with molecular simulations, visualizing motion is essential to understand molecular mechanisms, reaction pathways, or conformational changes. Molecular modelers often run simulations that yield extensive trajectories—collections of molecular conformations over time. But how do you convert raw trajectory data into a clean, informative animation that smoothly conveys the story told by those structures?
This is where SAMSON’s Play path animation comes in. If you’ve ever wanted to animate a simulation trajectory or interpolate between experimentally derived structures, this tool makes it approachable and efficient.
What Is a Path in SAMSON?
In SAMSON, a Path is a node that stores a trajectory. This could be from a molecular dynamics simulation or a manually created conformational transition between two or more structures. The Play path animation applies movement over a selected trajectory and brings the molecular motion to life over a chosen animation segment.
Creating a Smooth Molecular Animation
To play a path in SAMSON:
- Select the path(s) you wish to animate (these could be conformational changes, reaction coordinates, or full trajectories).
- In the Animation panel of the Animator, double-click the Play path animation effect.
- The entire path is automatically mapped between two keyframes in the timeline. Adjust the positions of these keyframes to control playback timing.
By default, SAMSON smooths the animation between the trajectory frames if the number of animation frames doesn’t match the number of trajectory frames. This is useful if you want a fluid motion, especially when interpolating between spatially distant conformations. However, you can disable smoothing if precise frame-to-frame transitions are important—for example, if each trajectory frame has physical significance.
Tweaking the Behavior
The animation offers properties that go beyond basic playback. One key feature is the Easing curve, which controls the interpolation style between frames. For instance, you can make the motion start slowly, accelerate, and then decelerate—just like real molecular motions.
Why Use It?
Many molecular modelers struggle to produce clear and synchronized visualizations of dynamic molecular processes. The Play path animation in SAMSON is particularly helpful when you:
- Want to create a clean visual representation of a simulation’s progression.
- Need to compare multiple trajectories side by side (synchronized path playback supported).
- Are preparing illustrative animations for presentations or teaching materials.
Here’s a quick example of the animation effect in action:
You can update properties anytime by selecting the animation in the animation timeline and opening the Inspector. Don’t forget you can freely move the keyframes to adjust the timing of the animation sequence.
To learn more, visit the official SAMSON documentation on the Play path animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.