notes/FIGURE_DATA.md

Data behind the paper figures — DO NOT DELETE (checked 2026-10-02)

Rendering: matplotlib (plots), ChimeraX 1.8 (/n/netscratch/.../software/chimerax/root/usr/libexec/UCSF-ChimeraX/bin/ChimeraX, headless) for maps / morph movies. Bead models can render any conformation from their checkpoints.

planned figure	content	data (all present)	still to compute
Fig. 1 method overview	hierarchy schematic + example	results/synth_hier* (classes, decisions), data/synth_hier/gt.npz	schematic drawing
Fig. 2 benchmarks	AU-FSC bars (draft done: scripts/fig_benchmark.py reads Table 1 from main.tex → results/figures/benchmark.{pdf,png,json}) + per-query curves	results/official/*/score_*.json (mean + per_query; older compact files lack per_query), paired_tests.json	rerun after last Spike cell
Fig. 3 conformational landscapes + morphs	IgG-1D hinge circle, IgG-RL Fab, Spike RBD: latent landscape + trajectory movie	results/*_test_results.h5 (z, dm, R, t), */landscape_traj_ca.pdb, */hinge*_traj_ca.pdb, */states_by_dm1_ca.pdb, scored state maps results/official/*/extp_*/state###.mrc (100 per method), checkpoints checkpoints/*/last_checkpoint.pth	ChimeraX morph movie / volume series per dataset
Fig. 4 composition	Ribosembly assembly states + assembly graph	results/ribo_v0c/level1r_class*.mrc (16 class maps), level1_relate.json, ribo_v0c_rigid2*/particle_explain_mapnull*, hier_decide*	draft done: scripts/fig_ribo.py (render via scripts/chimerax_offscreen.sh, compose) → results/figures/ribo/ribo_graph.{pdf,png}
Fig. 5 calibration	BIC vs bead null vs map null	results/figures/calibration_contrast.{json,pdf}	done
Fig. 6 EMPIAR-10180	domains on the map, labelled fractions, motion of HELICASE / SF3b on the labelled subset, maps along the principal motion, RELION comparison	results/e10180_rigid_gate/particle_explain_mapnull_full_d*.npz (labels + local rotvecs per particle), validate_labels_mapnull.json, results/e10180_rigid_gate_test_results.h5, RELION bodies results/relion_multibody/, raw data/real/empiar10180*	PCA of labelled local rotations → reconstructions binned along PC1 (GPU, ~1 h) → ChimeraX morph
Fig. 7 second real dataset	EMPIAR-10076 composition (L17-depleted 50S)	download in progress → data/real/empiar10076	full pipeline