Player. The trajectory comes from the ATLAS MD ensemble for this chain (3 replicates × 1000 frames, subsampled to 250 evenly for the browser). Play/pause, speed (0.25–2×), and the frame slider all act on the same ensemble. Smooth interpolates between frames with a spline for less jitter (purely visual, no data added).

Flexibility. Colors the cartoon by per-residue RMSF (root-mean-square fluctuation) measured across the ensemble. Blue = rigid; red = flexible. Tight folded cores and well-formed helices are typically blue; loops and termini are red. Replaces the default rainbow coloring while on.

Contacts. Cylinders connect Cα pairs that are within the distance threshold (d≤) in at least the chosen fraction of frames (p≥). Color encodes sequence separation: yellow = near in sequence (i,i+2 to i+5; helical / strand-internal), red = far in sequence (tertiary contacts crossing the fold). Thickness grows with probability. The distance slider triggers a server recompute on release; the probability slider filters the returned list locally. Lower p to surface transient contacts; raise d to catch looser associations.

Ellipsoids. One per Cα, drawn from the eigendecomposition of that residue's 3×3 position covariance over the ensemble. Axis lengths are √(eigenvalues); axis directions are the eigenvectors. A long thin ellipsoid means the residue wobbles much more in one direction than the others (anisotropic flexibility); a roundish one means it moves about equally in every direction. Color repeats the flexibility scale, so size and hue both reflect mobility. The scale slider only resizes them for visibility.

PCA mode. Pauses the trajectory and instead sweeps the structure along the dominant principal-component eigenvector of the ensemble's Cα covariance, with amplitude set by √(explained variance). Mode 1 is the largest concerted backbone motion; modes 2 and 3 are the next two. Useful for seeing the protein's overall shape of flexibility (e.g., a hinge bend that's smeared across many trajectory frames). Only Cα atoms move; side-chain and other backbone atoms stay at the mean structure.

Metrics. The panel below scores the selected model's sample ensemble against the full ATLAS reference (the same v1 panel the leaderboard uses, not just the 250-frame subsample shown in the viewer). RMWD (root-mean Wasserstein distance, Å) is the per-atom 2-Wasserstein between Gaussian approximations of the two ensembles, split into a mean (how far the average positions sit apart) and a variance (how differently they fluctuate) component; lower is closer. RMSF correlation is the Pearson r between per-residue fluctuation profiles (higher is better). MD-PCA W₂ is the 2-Wasserstein in the reference's top-2 PCA basis (Å, lower better). The contact Jaccards compare which weak / transient CA-CA contacts each ensemble forms (higher is better; "n/a" when the contact set is empty). First load computes server-side and caches.

All overlays read from the per-chain reference cache (~/.cache/premval/atlas/references/….npz). Recompute with premval prepare-refs --chains 6nl2_A --overwrite.