Live refinement also runs on a broker without a GPU, on the CPU and slower, and the run's deadline
or cancel can cut it. Description only; regenerated broker/gen (Rugnux_live_refinement.h), the
frontend client (types.gen.ts, zod.gen.ts), broker/redoc-static.html and the python client doc
page - each differs from before only in this description.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 53d06c6e221fa1cf776822965560fb990cc69c73)
The refinement of a placed model gets the run's cancel flag (RefinementSettings::cancel, through
CancelFlag::RunFlag), so the broker's deadline or a cancel - and Ctrl+C in rugnux - cuts a running
refinement short with what its finished trials found. RefinementResult::cancelled goes to the live
status as rugnux_live_refinement.cancelled (API, regenerated clients) and to the step's note.
Hero: once refined, the model card's headline is "R-work / R-free, refined" (e.g. 0.32 / 0.35), its
green/red still the placement verdict, the placement and fit in the context line.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 395016a30c2bc2aa26fdf2cec2ced9cebe6fad80)
The live run refines a placed model as `rugnux` does (ProcessConfig::refine), after every decision
and before the end message; a cut before it starts leaves it out, as the model. The writer still
gets the placed model; the refined one stays with the broker.
API (broker/jfjoch_api.yaml):
- rugnux_live_model.refinement (rugnux_live_refinement): performed, reason, on_gpu, seconds, r_work,
r_free, rmsd_bonds_A, rmsd_angles_deg, blob_count, blobs (at most 50, rugnux_live_blob: kind, x, y,
z, peak_sigma, volume_A3, nearest_atom, nearest_atom_distance_A)
- rugnux_live_status.refined_model
- /rugnux/model.cif and /rugnux/map.ccp4 take stage=placed|refined, by default the refined model
where there is one; the anomalous map stays on the placed model's phases (the refined
coefficients carry none).
Regenerated broker/gen, frontend/src/client, redoc, and the python client docs (which also brings
the hero fields and rugnux_live_model it was missing).
Frontend: the model card keeps its green/red and gets "R-free 0.xx (refined)" as its context line,
"refining..." while the step runs; the model section adds refined R-free and blob tiles; Mol*
shows the refined model and maps, with the blobs as small spheres coloured by reading (switch, off
at first). The Refinement step is in the timeline like any other.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 3b47fb9a53b7dfad1c1ed289e169094c8d3d9d3e)
leonarski_f