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leonarski_fandClaude Fable 5.1 7782e304ed

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RESULT-CHANGING: Refinement: atoms gridded out to a density of 1e-4 e/A^3, not 1e-5

The refinement's density calculators (the CPU engine's, the GPU engine's and the map gradient's) cut every
atom's density at an absolute 1e-4 e/A^3 of its blurred density instead of gemmi's default 1e-5. The radius,
the gather's box and the gradient's box all follow from it, so the structure factors, the gradients and with
them the refined model change in the last digits. Molecular replacement's and the validation's own
calculators keep gemmi's default.

Where this sits against other programs' defaults, which are relative to the atom's own peak density: cctbx
resolves phenix.refine's wing_cutoff to 1e-3 of the peak below 5 A (1e-4 above), X-PLOR's ELIM 7 is e^-7 of
the peak and SFALL's VDWR 2.5 about 2e-3 of it. For carbon at B + blur of 20-120 A^2 an absolute 1e-4 is
6e-5 to 6e-4 of the peak - still stricter than any of them.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu

2026-10-27 11:04:46 +01:00

.gitea/workflows

CI: the documentation goes to rugnux/gitea-pages only when a release is created

2026-10-26 15:46:17 +01:00

acquisition_device

v1.0.0.rc-161 (#71 )

2026-08-13 17:03:10 +02:00

broker

broker: redoc regenerated from the merged API (blob distance optional, live refinement on the CPU too)

2026-10-26 15:39:21 +01:00

common

jfjoch_writer: the live refinement's model, maps and blobs are written beside the master file

2026-10-26 15:50:40 +01:00

compression

v1.0.0-rc.175 (#85 )

2026-10-16 15:34:43 +02:00

detector_control

v1.0.0-rc.175 (#85 )

2026-10-16 15:34:43 +02:00

docker

1.0.0-rc.174 (#84 )

2026-10-06 14:03:18 +02:00

docs

docs: front page names the reimplemented algorithms and generative AI in the licence section, and says the licences' sharing condition plainly

2026-10-27 11:04:46 +01:00

etc

v1.0.0-rc.166 (#76 )

2026-09-02 21:17:31 +02:00

fpga

v1.0.0-rc.180: VERSION and update_version.sh

2026-10-24 16:57:12 +02:00

frame_serialize

jfjoch_writer: the live refinement's model, maps and blobs are written beside the master file

2026-10-26 15:50:40 +01:00

frontend

rugnux live: a score that is not finite is left out of the status, not sent as null

2026-10-26 15:38:58 +01:00

gemmi_gph

Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib

2026-10-25 07:20:32 +01:00

image_analysis

RESULT-CHANGING: Refinement: atoms gridded out to a density of 1e-4 e/A^3, not 1e-5

2026-10-27 11:04:46 +01:00

image_puller

v1.0.0-rc.178 (#88 )

2026-10-21 11:20:01 +02:00

image_pusher

v1.0.0-rc.178 (#88 )

2026-10-21 11:20:01 +02:00

include

v1.0.0-rc.133

2026-03-26 20:50:33 +01:00

jungfrau

v1.0.0-rc.153 (#63 )

2026-06-23 20:29:49 +02:00

licenses

fast-feedback-indexer vendored in image_analysis/indexing/fast-feedback-indexer instead of fetched

2026-10-25 19:58:38 +01:00

preview

v1.0.0-rc.179 (#90 )

2026-10-24 14:52:29 +02:00

reader

NXmx: the unit cell's e.s.d.s are saved as /entry/sample/unit_cell_esd

2026-10-26 15:50:40 +01:00

receiver

broker: rugnux live publishes its result before the run's teardown, which goes on beside the end message

2026-10-26 21:13:17 +01:00

rugnux

Rotation tail: the final merge made ahead on a spare card, in the groups the run is expected to adopt

2026-10-27 05:57:57 +01:00

tests

Error model: ISa is reported only where b is the solution of a fit - not beside a clamped a, not when b was held at zero, and on stills under the same rule

2026-10-26 23:09:38 +01:00

tools

rugnux: a placed model is refined by default - giving a model is the opt-in

2026-10-26 01:38:24 +01:00

viewer

rugnux: a placed model is refined by default - giving a model is the opt-in

2026-10-26 01:38:24 +01:00

writer

jfjoch_writer: the live refinement's model, maps and blobs are written beside the master file

2026-10-26 15:50:40 +01:00

xds-plugin

v1.0.0-rc.175 (#85 )

2026-10-16 15:34:43 +02:00

.gitattributes

v1.0.0-rc.153 (#63 )

2026-06-23 20:29:49 +02:00

.gitignore

Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib

2026-10-25 07:20:32 +01:00

.readthedocs.yaml

version 1.0.0-rc.25

2024-11-22 21:25:20 +01:00

CLAUDE.md

fast-feedback-indexer vendored in image_analysis/indexing/fast-feedback-indexer instead of fetched

2026-10-25 19:58:38 +01:00

CMakeLists.txt

fast-feedback-indexer vendored in image_analysis/indexing/fast-feedback-indexer instead of fetched

2026-10-25 19:58:38 +01:00

CONTRIBUTING.md

version 1.0.0-rc.27

2024-12-02 21:17:14 +01:00

gen_python_client.sh

v1.0.0.rc-161 (#71 )

2026-08-13 17:03:10 +02:00

gitea_create_release.py

v1.0.0-rc.94

2025-10-25 22:05:47 +02:00

gitea_upload_file.py

v1.0.0-rc.156 (#66 )

2026-07-03 19:18:56 +02:00

LICENSE

v1.0.0-rc.175 (#85 )

2026-10-16 15:34:43 +02:00

make_doc.sh

v1.0.0.rc-161 (#71 )

2026-08-13 17:03:10 +02:00

README.md

1.0.0-rc.174 (#84 )

2026-10-06 14:03:18 +02:00

THIRD_PARTY_NOTICES.md

Refinement restraints: metal ions bound to their donors by the model's LINK records

2026-10-26 01:38:24 +01:00

update_version.sh

v1.0.0-rc.175 (#85 )

2026-10-16 15:34:43 +02:00

VERSION

v1.0.0-rc.180: VERSION and update_version.sh

2026-10-24 16:57:12 +02:00

README.md

Jungfraujoch

Application to receive and analyse data from the PSI JUNGFRAU and EIGER detectors, together with rugnux, its program for processing stored diffraction data - rotation and serial, macromolecular and small-molecule - from images to merged reflections.

All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.