A molecular trajectory can produce many useful measurements: distances, energy values, RMSD, radius of gyration, and solvent-accessible surface area, to name a few. The difficulty is that looking at each measurement separately may hide how they relate. Does a distance increase as energy changes? Do large structural deviations occur alongside changes in compactness? A custom scatter plot brings two saved scalar analyses together so you can investigate those questions directly.
In SAMSON’s Path Analyzer, each point in a custom scatter plot represents a sampled pair of scalar values. Rather than reading two separate curves and trying to mentally match their behavior, you can inspect the measurements in a shared observable space. Patterns may reveal a relationship, an opposing trend, groups of samples, or a less straightforward shape that deserves closer examination.
Start with a question, not just two measurements
A useful scatter plot begins with a scientific question. For example, you might ask whether a particular distance tends to change alongside energy, whether RMSD varies with radius of gyration, or whether solvent-accessible surface area changes with a distance of interest. These examples are not conclusions: they are pairs of observables to examine. The plot helps you see how the sampled values are arranged, but interpreting what that arrangement means still depends on the molecular system and the question you are asking.
Pair selection matters. Two measurements are most informative when there is a reason to expect a connection between them. If the plot looks like an unstructured cloud, that is still useful information: the chosen measurements may not show a simple relationship over the sampled data, or the relationship may require more context. A curved shape, separated groups, or a dense region can also prompt a closer look instead of being reduced to a single summary number.
Build the comparison in Path Analyzer
- Open Path Analyzer.
- Create or reuse two saved scalar analyses in the Analysis Tray.
- Choose Custom scatter under Observable.
- Select exactly two saved scalar analyses in the tray, then click Add Scatter.
Custom scatter is a derived analysis, so its inputs come from the Analysis Tray rather than from direct atom selections. Both source analyses need to be scalar analyses. This makes the key preparation step simple but important: make sure the two analyses you want to compare are saved and available in the tray before adding the plot.
Read the plot with the trajectory in mind
Each point summarizes one sampled pair of values. Look first for broad structure: Is the cloud compact or spread out? Does it appear to slope upward or downward? Are there distinct groups or unusual points? These observations can help you decide what to investigate next, but a visual pattern by itself does not establish causation or explain the underlying molecular mechanism.
Frame linkage can add useful context. If both source analyses come from the same path and remain frame-linked, the scatter plot can stay connected to the current frame. When the two sources are frame-linked, clicking a point can move the path to its corresponding frame. That can help connect a point in observable space with the molecular structure it represents. For meaningful frame-level interpretation, check that the source analyses belong to the intended path and retain their frame linkage.
Once you have explored the scatter, it can serve as a starting point for a more focused view. The Path Analyzer documentation suggests using scatter plots before creating a 2D density map or an Energy landscape. In practice, the scatter plot helps you decide whether the pair of observables is worth examining in more detail.
The goal is not to make every pair of measurements tell a clear story. It is to make comparisons easier to inspect, identify patterns worth following up, and connect sampled values back to frames when the analyses support that link. For setup details, see the Custom Scatter documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.