Add v0.4.0 3D backbone reconstruction section to README

- New 'alphadynamics rebuild' CLI subcommand (NeRF backbone PDB)
- Python API: trajectory_to_pdb, torsions_to_backbone, diagnostics
- Cross-link to v0.4.0 PyPI release

README.md

@@ -62,7 +62,32 @@ Or as a one-liner for power users:
 alphadynamics predict --sequence AAAY --n-ensemble 16 --rollout-steps 2500 --plot --plot-html -o traj.npz
 ```
 
-Or from Python:
+### 3D backbone reconstruction (NEW in v0.4.0)
+
+Convert torsion `.npz` to multi-model PDB you can open in PyMOL / VMD / ChimeraX:
+
+```bash
+alphadynamics predict --sequence KLVFFAE --output klvffae.npz
+alphadynamics rebuild klvffae.npz -s KLVFFAE -o klvffae.pdb --diagnostics
+pymol klvffae.pdb        # animate the trajectory
+```
+
+From Python:
+
+```python
+from alphadynamics import predict_torsion_ensemble, trajectory_to_pdb
+traj = predict_torsion_ensemble("KLVFFAE", n_ensemble=4, rollout_steps=200)
+trajectory_to_pdb(traj[0], "KLVFFAE", "klvffae.pdb")
+```
+
+Backbone heavy atoms only (N, Cα, C, O); deterministic NeRF reconstruction
+(Parsons 2005) with Engh-Huber 1991 standard bond geometry. No ML, no training.
+
+> ⚠️ Torsion errors accumulate along the chain; for long peptides
+> (N > ~50) end-to-end displacement may be substantial. Use as
+> diagnostic visualization, not high-resolution structure prediction.
+
+### Or from Python (raw API):
 
 ```python
 from alphadynamics import predict_torsion_ensemble