RMSD#
The RMSD analysis tracks how much a measured set deviates from the first frame after each frame has been aligned using a fit set. It is one of the most useful ways to separate overall rigid-body motion from internal structural change.
Adding the plot#
- Open Path Analyzer.
- Choose RMSD in Observable.
- Choose a Path.
- Define a Measured set and a Fit set.
- Click Add Time Series or Add Histogram.
Inputs#
- Two atom-containing selections are required.
- The Fit set is used to align each frame to the first frame.
- The Measured set is then compared with the first-frame measured set after alignment.
Views#
- Time series: follow structural deviation frame by frame.
- Histogram: inspect the distribution of sampled RMSD values.
Key equation#
After aligning each frame with the chosen fit set, Path Analyzer compares the measured set with the first frame:
\[
\operatorname{RMSD}(t)=
\sqrt{
\frac{1}{N}
\sum_{i=1}^{N}
\left\|
\tilde{\mathbf{r}}_i(t)-\mathbf{r}_i(0)
\right\|^2
}
\]
Here, \(\tilde{\mathbf{r}}_i(t)\) denotes the measured-set positions after fitting frame \(t\) onto frame \(0\).
Interactions#
- Clicking a point moves the path to the corresponding frame.
- Double-clicking a point selects the measured features in SAMSON.
Tip
- Use a stable core, backbone, or binding-site scaffold as the fit set.
- Use a more flexible region as the measured set when you want to isolate local rearrangements.
- Pair RMSD with Radius of gyration, Distance, or Energy to understand what drives large excursions.