A molecular structure can look almost unchanged in two snapshots and still undergo an important local motion: a hinge opens, a loop bends, or two structural regions rotate relative to one another. The challenge is turning that visual impression into a measurement you can follow across a trajectory. A single angle provides a compact way to describe how three selected parts of a molecule move in relation to each other.
In SAMSON’s Path Analyzer, the Angle observable measures the angle formed by three selections: Group A, a middle selection called the Vertex, and Group C. Think of the vertex as the point of a hinge. At each frame, the analysis forms one vector from the vertex toward Group A and another from the vertex toward Group C, then calculates the angle between them. Following that value along a path can help answer questions such as: Does this region open gradually? Does it switch between distinct conformations? Is a motion brief or sustained?
Choose selections that match the question
The most important modeling choice is not the plot type; it is what each selection represents. For a highly local measurement, use one atom for each point. This makes the angle sensitive to the positions of those specific atoms. For a broader, coarse-grained description, select groups of atoms that represent the structural regions whose relative orientation you want to track.
Path Analyzer converts each selection into one representative position at every frame. A single-atom selection uses that atom’s position. A multi-atom selection uses the group’s center of mass, calculated by weighting each atom’s position by its mass. This is useful when you want to summarize a larger region with one point, but it also means that internal rearrangements within the group are not shown directly. Two groups with very different internal shapes can have similar centers of mass, so choose group boundaries with the question in mind.
Keep the middle selection at the structural location you want to treat as the hinge or vertex. The other two selections should lie on opposite sides of that point in a way that makes the motion interpretable. If you are studying a domain hinge, for example, representative selections from the two domains and a suitable connecting region may provide a more meaningful readout than three nearby atoms. The selections must contain atoms, and the representative positions should not coincide with the vertex position: the angle formula relies on two nonzero vectors.
Read the plot as a measurement, not a verdict
Add a Time Series to see how the angle changes along the path. If the path contains time values, time is used on the horizontal axis; otherwise, the horizontal axis shows frame indices. A sustained change can indicate a persistent geometric rearrangement, while a short-lived excursion may point to a transient event worth inspecting in the structure. The angle alone does not explain why the motion occurred, so use it to identify when something changes and then inspect the corresponding structures.
A Histogram answers a different question: which angle values were visited, and how often? It can reveal whether a path spends time in one broad range or samples multiple ranges. However, a histogram does not preserve the order of frames. If the sequence matters—for example, whether opening happened before closing—use the time series as well.
The calculation uses the normalized dot product of the two vectors, followed by the inverse cosine. In practical terms, it reports the geometric opening between the two directions from the vertex. It is a single scalar description, not a complete account of a three-dimensional motion: different structures can share the same angle. Treat it as one interpretable coordinate, and combine it with other saved scalar analyses when a larger picture is needed. Path Analyzer documentation points to Custom scatter and Energy landscape for combining analyses.
Quick setup
- Open Path Analyzer.
- Choose Angle under Observable, then select a path.
- Define Group A, Vertex, and Group C, making sure all three selections contain atoms.
- Choose Add Time Series to follow the motion, or Add Histogram to examine the distribution of angles.
A useful angle plot begins with a clear structural question: which two parts are moving, and around what point? Thoughtful selections make the resulting curve easier to interpret—and easier to explain to someone else.
For the full details, see the Angle analysis documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.