Reproduction guide, env specs, run logs, structures, CryoSTAR work dirs, latent sources (part 5)
3a467f6 verified | # 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 | | |