Density Curve#
The Density curve analysis turns one saved scalar analysis into a smooth one-dimensional density estimate. It is perfect for turning a noisy distribution of values into an easy-to-read landscape of preferred states.
Adding the plot#
- Open Path Analyzer.
- Create or reuse a saved scalar analysis in the Analysis Tray.
- Choose Density curve in Observable.
- Select exactly one saved scalar analysis in the tray.
- Click Add Density Curve.
Inputs#
- This is a derived analysis: it uses the Analysis Tray instead of direct atom selections.
- The source analysis must provide a scalar value series, such as Distance, RMSD, Energy, or Radius of gyration.
View#
- Density curve: a smooth density estimate as a function of the source-analysis value.
Key equation#
Path Analyzer builds the density curve from the sampled scalar values \(\{x_i\}_{i=1}^{N}\) using a Gaussian kernel density estimate of the form
\[
\hat{f}(x)=\frac{1}{Nh}\sum_{i=1}^{N}
\frac{1}{\sqrt{2\pi}}
\exp\!\left(-\frac{1}{2}\left(\frac{x-x_i}{h}\right)^2\right)
\]
where \(h\) is the automatically chosen bandwidth.
Tip
- Use density curves when a histogram feels too jagged or too dependent on binning.
- Density curves summarize value populations, so they are not frame-linked.
- They are especially useful before building a 2D density map or an Energy landscape.