Or we can look at the unfolding, the force profile, and the contact maps together:
Animations are always really useful, but if we want to classify trajectories, or have a quick overview, it is better to summarize all the frames in one plot. ConAn has several time-encoded contact maps, for example, on the total interaction time:
- Around ~15-25%: residues 0-10 losing contact with 10-20 and 60-70.
- Around ~40%: residues 25-70 losing contact with each other.
- Around ~70%: residues 20-40 losing helicity.
In case you are studying folding instead (or non-native intermediates during unfolding), you will also find the opposite plot interesting, i.e., time of the first encounter:
β4 forms a short-lived helical intermediate around 150 ns.
If we had several different trajectories, any of these 3 statistics (although probably the total interaction time would be the best) could be a good basis for clustering them, either "by eye" or by some more sophisticated method.