A molecular trajectory can contain hundreds or thousands of frames, but a visual inspection may not tell you exactly when a hinge opens, a loop bends, or two structural regions change their relative orientation. Measuring the distance between two groups is not always enough: a hinge can rotate while its endpoints remain at similar distances. A three-group angle gives you a simple geometric quantity to follow through the motion.
What the angle measures
In Path Analyzer, the Angle observable measures the angle formed by three selected groups along a path or trajectory. The middle selection is the vertex. Think of the groups as points A, V, and C: the measured angle is between the vectors from V to A and from V to C.
At each frame, the calculation is the standard vector angle:
θ(t) = arccos(((pA − pV) · (pC − pV)) / (‖pA − pV‖ ‖pC − pV‖))
This makes the measurement useful for questions such as: does a domain open during the path? Does a loop bend more in some frames than others? Is a local arrangement changing gradually or in a few distinct steps? It gives you a scalar value to inspect, rather than relying only on the apparent shape of an animation.
Choose groups that match the question
The group definitions matter. If a selection contains one atom, its atomic position is used. If it contains multiple atoms, Path Analyzer represents the selection by its center of mass. In other words, a multi-atom selection becomes one representative point before the angle is calculated.
This is useful when you want a coarse-grained description of larger structural regions, but it also sets a limit on what the result means. The angle is between representative positions; it is not a direct measurement of every bond or an averaged orientation of the groups. A large selection may hide local changes, and movement of atoms within a selection can shift its center of mass. For a highly local question, use single atoms or small selections. For a broader hinge-like motion, larger groups can provide a more compact descriptor.
Build a readable trajectory plot
- Open Path Analyzer.
- Choose Angle under Observable, then choose the path to analyze.
- Define Group A, the middle Vertex, and Group C.
- Add a time series to see how the angle changes across the path, or add a histogram to examine which angle values occur.
A time series is the better first view when the question is about timing: where does the angle begin to change, and does it settle or fluctuate? A histogram answers a different question: which values are visited, and are values concentrated in one region or spread across several? A histogram alone does not show the order of events, so use the time series when sequence matters.
For the horizontal axis, Path Analyzer uses time when the path provides time values; otherwise, it uses frame indices. Keep that distinction in mind when describing a plot. Frame number and elapsed time are not interchangeable unless the trajectory’s timing information supports that interpretation.
Make the measurement useful
Before interpreting a large change, check whether the selected groups represent the motion you care about. Try to place the vertex at the structural point around which the bend is expected, and make the outer groups reflect the two sides of that bend. If the angle changes, inspect the corresponding frames in the molecular view: the plot tells you that the geometry changed, while the structure helps you understand what moved.
Finally, treat one angle as one piece of evidence. If the motion involves another property, such as a distance or energy-related scalar, Path Analyzer’s Custom scatter or Energy landscape can help compare saved scalar analyses. The goal is not to make a single number explain the whole trajectory, but to turn a specific structural question into a quantity you can inspect and compare.
For the full details, see the Angle analysis documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.