tf_z, rf_z, mr_d_min, the placed model's R-factors, CC, map and anomalous sigmas, the rigid
body's move, the refinement's R-factors and rmsds, and the headline d_min are set only where
finite (llg_z and null_sigma already were). nlohmann writes NaN/inf as null, which the page's
"!== undefined" checks let through to .toFixed(), and which the zod schema rejects for the
required blob distance - a blob with no atom within 12 A has an infinite one. That distance
is now optional (jfjoch_api.yaml; C++ model and frontend client regenerated), absent then.
The model cards test for != null, so a null that arrives anyway does not take the page down.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 62ff026aa507e5bda1daa5aa079f32fb5c21f16e)
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)
Under the header of the Rugnux live page, four big-number cards in the manner of jfjoch_viewer's merge
statistics window: Resolution (d_min of the merge), ISa, Space group (short symbol, screw axes
subscripted) and the model. The model card shows the fit over random orientations - R-work of the placed
model below its random-orientation null, in sd - which is the test rugnux places a model by, both for
molecular replacement (after the TFZ/LLG-Z gate) and for a model that fits where it is. The card is green
where rugnux placed the model (placement MR or RIGID_BODY), red where it did not (with MR's reason), grey
where no model was uploaded; no threshold of its own. "—" while the run is going, "searching…" during
the MR step.
/rugnux/status gains `space_group`, `d_min` and `isa` (set with the result; absent until then, isa also
where the error model did not determine it), filled from ProcessResult in RugnuxThread with the values
the summary's Space group, Resolution and Signal rows print.
Generated code regenerated from jfjoch_api.yaml: broker/gen (cpp-pistache-server 7.20.0), the TypeScript
client (npm run openapi) and broker/redoc-static.html. Python client not regenerated.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit fcc019707751aab9d8c9f349309eeadcf364b9c2)
/rugnux/status gains `model` (rugnux_live_model) - placement (RIGID_BODY/MR/NOT_PLACED), R-work and
R-free of the placed, unrefined model, CC(model, data), R-work over its random-orientation null, mean
2mFo-DFc at the atoms, the rigid body's move, molecular replacement's decision, group, copies,
TFZ/RFZ/LLG-Z and search resolution, and the strongest anomalous site - taken from
ProcessResult::model_validation and ::model_prior (LiveModel). `anomalous_signal` says the summary's
"Anomalous" row reports usable signal (CC_anom > CC_ANOM_SIGNAL, now a named constant shared with the
report), so the viewer can show the anomalous map by default only then.
The step that placed the model (Molecular replacement, or Model validation) now carries notes: what
MR placed and its TFZ/RFZ, R-work/R-free (unrefined) and CC(model, data), the rigid-body move.
Generated code regenerated from jfjoch_api.yaml: broker/gen (cpp-pistache-server), the TypeScript
client (npm run openapi) and broker/redoc-static.html. Python client not regenerated.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit f602e931dc6afcccb3767b8c6df87650d9496033)
* Rugnux: Processes serial crystallography data from XFELs - SACLA (MPCCD), PAL-XFEL and European XFEL (CXI), LCLS (XTC) and SwissFEL Alvra (JUNGFRAU with a CrystFEL module geometry) - with several files or Jungfraujoch master files merged in one run (`rugnux *_master.h5`).
* Rugnux: Stills processing takes a known unit cell and space group as a starting point, finds the beam centre (and, with a cell, the detector distance) from the images, detects the saturation level in other facilities' files and refines the placement of individual detector panels.
* Rugnux: The stills report gives R_split and CC1/2 from frame half-sets, comparable with CrystFEL.
* jfjoch_viewer: Opens the same XFEL file formats.
* Validation: A stills battery checks Rugnux against deposited structures from SACLA, PAL-XFEL, LCLS, European XFEL and SwissFEL.
* Rugnux: More reliable convergence of rotation scaling, and live molecular replacement starts as soon as the model is uploaded.
* jfjoch_broker: Initialize clears the previous dataset's bearer tokens, image buffer and live Rugnux status, and a slow CUDA JIT cache is reported at start.
Reviewed-on: #88
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
leonarski_f