Custom Scatter

The Custom scatter analysis compares two saved scalar analyses directly against each other. It is one of the fastest ways to discover correlations, anticorrelations, clusters, or transition pathways in a user-defined observable space.

Adding the plot

1. Open Path Analyzer.
2. Create or reuse two saved scalar analyses in the Analysis Tray.
3. Choose Custom scatter in Observable.
4. Select exactly two saved scalar analyses in the tray.
5. Click Add Scatter.

Inputs

• This is a derived analysis: it uses the Analysis Tray instead of direct atom selections.
• The source analyses must be scalar analyses.
• If both analyses come from the same path and remain frame-linked, the scatter plot can stay connected to the current frame.

View

• Scatter: each point represents one sampled pair of scalar values.

Interactions

• When the two source analyses are frame-linked, clicking a point can move the path to the corresponding frame.

Tip

• Use pairs that answer a real scientific question, for example Distance vs Energy, RMSD vs Radius of gyration, or SASA vs Distance.
• Scatter plots are often the best starting point before creating a 2D density map or an Energy landscape.