A molecular trajectory can produce a long list of scalar measurements: distances, energies, RMSD values, radius of gyration, solvent-accessible surface area, and more. Looking at each measurement separately may reveal that it changes, but not whether two changes happen together. Does the structure become more compact as a particular distance increases? Do high-energy samples coincide with a specific range of RMSD? A custom scatter plot helps you investigate these questions directly.
In SAMSON’s Path Analyzer, Custom scatter compares two saved scalar analyses. Each plotted point represents one sampled pair of values. Instead of scanning two separate curves or tables, you can see how the measurements relate across the samples.
Start with a question, not just two measurements
The most useful plot is one that helps answer a concrete question about your system. For example, you might compare Distance vs Energy to see whether samples with a particular distance tend to have different energy values. Or compare RMSD vs Radius of gyration to explore how structural deviation relates to compactness. SASA vs Distance can help you inspect whether changes in a distance accompany changes in solvent-accessible surface area.
These plots show relationships in your sampled data; they do not, by themselves, establish that one measurement causes another. A visible trend is a useful observation to investigate, not a complete explanation of the molecular mechanism.
Build the comparison
- 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: it uses the saved analyses in the Analysis Tray rather than direct atom selections. Both inputs need to be scalar analyses. This makes it useful when the measurements you want to compare have already been calculated and saved.
Read the shape before drawing conclusions
Look first at the overall arrangement of points. A sloping band can suggest that the values tend to change together or in opposite directions. Separate groupings may point to distinct regions of sampled observable space. A broad cloud may indicate that the relationship is less straightforward, while isolated points are worth checking in context. These are visual clues, not automatic diagnoses: consider the underlying molecular system and how the samples were generated before interpreting them.
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 analyses are frame-linked, clicking a point can move the path to its corresponding frame. That connection makes it easier to inspect a point of interest in the molecular structure rather than treating it as an abstract pair of numbers.
Use the scatter as a starting point
A scatter plot is often a helpful first look at two observables before moving on to a 2D density map or an Energy landscape. The key is to choose measurements that connect to a scientific question, then use visible patterns to decide what deserves closer examination.
For setup details, see the Custom Scatter documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.