A protein can look almost unchanged in a structure overlay and still undergo an important local movement. A domain may swing, a loop may bend, or a hinge may open gradually along a conformational path. The practical challenge is turning that movement into a measurement you can follow across frames—not just a visual impression from two snapshots.
One simple way to do this in SAMSON is to track an angle defined by three selections. The middle selection is the vertex; the other two define the arms. As the structure changes along the path, the angle reports how those arms open or close around the vertex. This makes it useful for monitoring a hinge-like motion with a single scalar value.
Choose points that represent the motion
Start by deciding what you want the angle to describe. For a local bend, three individual atoms can provide a focused measurement. For a broader domain movement, select larger atom-containing groups so the measurement reflects the relative positions of structural regions rather than the motion of one atom.
Path Analyzer converts each selection into one representative position at every frame. A selection containing one atom uses that atom’s position. A selection containing several atoms uses their center of mass. The angle is then calculated between the two vectors that run from the vertex position to the positions of Group A and Group C.
This detail matters when choosing selections. A multi-atom group gives you a coarse-grained descriptor: it summarizes a region by one position rather than tracking every atom’s local geometry. That can make a domain-scale motion easier to interpret, but it also means the result depends on which atoms you include. For a highly local question, single atoms may be more appropriate; for a broad hinge movement, larger groups may provide a steadier structural reference.
Build the analysis
- Open Path Analyzer.
- Set Observable to Angle.
- Choose the path you want to analyze.
- Define Group A, Vertex, and Group C, in that order.
- Choose Add Time Series to follow the angle along the path, or Add Histogram to inspect the distribution of angles visited.
The order of the selections is important: the second selection is the vertex. A useful check before interpreting a plot is to confirm that the vertex lies at the structural location you intend to monitor and that the other two groups sit on opposite sides of the motion you care about.
Read the plot as a structural story
A time series is useful when you want to see when a bend or opening develops. A sustained change can indicate that the relative orientation of the two arms has changed along the path; smaller variations may show local fluctuations. Compare the plotted values with the corresponding structures when a change is surprising, since a single angle describes only the geometry of these three representative positions—not every detail of the surrounding molecule.
The x-axis depends on the path data. If the path provides time values, Path Analyzer uses time; otherwise, it uses frame indices. Keep that distinction in mind when comparing analyses or describing when a motion occurs.
A histogram answers a different question: which angle values appear across the sampled path, and how often? It can help distinguish a path that visits a narrow range from one that samples a broader range, but it does not preserve the order of events. Use the time series to understand sequence and the histogram to summarize the distribution.
Finally, treat the angle as one descriptor, not a complete explanation of a molecular motion. If the hinge angle is only part of a larger structural change, it can later be considered alongside another saved scalar analysis using Custom scatter or Energy landscape.
For the full setup details and equations, see the Path Analyzer Angle documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.