RMSF

The RMSF analysis computes a fluctuation profile for the measured features after all frames have been aligned with a fit set. It helps identify flexible atoms, residues, segments, or other selected features.

Adding the plot

1. Open Path Analyzer.
2. Choose RMSF in Observable.
3. Choose a Path.
4. Define a Measured set and a Fit set.
5. Click Add Profile or Add Histogram.

Inputs

• Two atom-containing selections are required.
• The Fit set removes overall motion by aligning every frame before fluctuations are measured.
• The Measured set defines what is profiled.

Views

• Profile: show RMSF for each measured feature.
• Histogram: inspect the distribution of fluctuation amplitudes.

Key equations

After aligning all frames with the fit set, the atom-wise fluctuation is

\[ \operatorname{RMSF}_a= \sqrt{ \frac{1}{T} \sum_{t=1}^{T} \left\| \tilde{\mathbf{r}}_a(t)-\left\langle \tilde{\mathbf{r}}_a \right\rangle \right\|^2 } \]

If a displayed feature contains multiple atoms, Path Analyzer shows the average of the atom-wise RMSF values for that feature:

\[ \operatorname{RMSF}_{\mathrm{feature}}= \frac{1}{|\mathcal{A}_{\mathrm{feature}}|} \sum_{a\in\mathcal{A}_{\mathrm{feature}}}\operatorname{RMSF}_a \]

Interactions

• Double-clicking a profile point selects the corresponding feature in SAMSON.

Tip

• If you want residue-level RMSF, select residues or residue-based groups as measured features.
• If you want atom-level RMSF, use atom selections directly.
• RMSF is most informative when the fit set captures the stable part of the system well.