Contact Persistence#
The Contact persistence analysis resolves contacts pair by pair across the whole path. It can display a contact timeline heatmap and a persistence distribution, making it ideal for finding stable, intermittent, and transient interactions.
Adding the plot#
- Open Path Analyzer.
- Choose Contact persistence in Observable.
- Choose a Path.
- Define Group A and Group B.
- Set the contact Cutoff.
- Click Add Contact Timeline or Add Persistence Distribution.
Inputs#
- Two atom-containing selections are required.
- The cutoff is given in
A. - Contact pairs are built from the selected feature groups rather than from a single pooled atom list.
Views#
- Contact timeline: a heatmap showing whether each contact pair is present or absent at each frame.
- Persistence distribution: a histogram of contact occupancies.
Key equations#
For each contact pair \((u,v)\), the timeline stores a binary state
\[
s_{uv}(t)=
\begin{cases}
1, & d^{\min}_{uv}(t)<r_c \\
0, & \text{otherwise}
\end{cases}
\]
and the persistence shown in the distribution is
\[
p_{uv}=\frac{1}{T}\sum_{t=1}^{T}s_{uv}(t)
\]
How to read it#
- Highly persistent rows correspond to long-lived contacts.
- Sparse or patchy rows indicate intermittent contacts.
- Only contact pairs observed at least once are kept in the timeline.
Tip
- This analysis is especially useful for interfaces, hydrogen-bond-like proximity patterns, and gating motions.
- Choose residue-level or domain-level groups if you want readable row labels.
- Use it alongside Contacts: the series tells you how many contacts exist, while contact persistence tells you which ones.