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leonarski_f 90bbba33bc writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does 
The placed-model END block lost everything but the atoms, so the writer's _model.cif had no sequence
references, authors, software or secondary structure, and gemmi relabelled the subchains. The block now
also carries label_asym_id, label_entity_id and label_seq_id per atom and the input model's metadata as the
mmCIF categories gemmi writes without coordinates (metadata_mmcif), which the writer parses with gemmi and
puts back. The writer's _model.cif is now the same text as the one rugnux writes itself and as
/rugnux/model.cif serves. Older blocks without the new fields are read as before.

Test: a predicted myoglobin model through END -> CBOR -> writer gives byte-identical _model.cif/_model.pdb
to WritePlacedModel and to PlacedModelMmcif, with its _struct_ref, _entity_poly_seq, _audit_author,
_software and _struct_conf.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 29d752e6a107e3b8bc71ad6e9af0d81064966537)
2026-10-22 20:18:51 +02:00
..
ADUHistogram.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ADUHistogram.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
AssembleToPlane.cpp
Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
2026-10-21 10:29:07 +02:00
AssembleToPlane.h
Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
2026-10-21 10:29:07 +02:00
AutoIncrVector.h
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
AzimuthalIntegrationMapping.cpp
Dense per-pixel maps through the panel table (panel layout stage 1)
2026-10-21 10:26:30 +02:00
AzimuthalIntegrationMapping.h
Dense per-pixel maps through the panel table (panel layout stage 1)
2026-10-21 10:26:30 +02:00
AzimuthalIntegrationProfile.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
AzimuthalIntegrationProfile.h
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
AzimuthalIntegrationSettings.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
AzimuthalIntegrationSettings.h
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
BraggIntegrationSettings.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
BraggIntegrationSettings.h
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
BrokerStatus.h
v1.0.0-rc.129 (#36)
2026-03-05 22:13:12 +01:00
CheckPath.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
CMakeLists.txt
Merge branch 'panel-s3' into panel-s5
2026-10-21 11:27:31 +02:00
ColorScale.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
ColorScale.h
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
CompressedImage.cpp
v1.0.0-rc.40
2025-05-28 18:49:27 +02:00
CompressedImage.h
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
Coord.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
Coord.h
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CorrelationCoefficient.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
CorrelationCoefficient.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
CrystalLattice.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CrystalLattice.h
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CudaJitCache.cpp
CUDA JIT cache: a private one under /var/tmp when the default is unusable
2026-10-20 07:50:57 +02:00
CudaJitCache.h
CUDA JIT cache: a private one under /var/tmp when the default is unusable
2026-10-20 07:50:57 +02:00
CUDAWrapper.cpp
v1.0.0-rc.177 (#87)
2026-10-19 16:07:31 +02:00
CUDAWrapper.cu
v1.0.0-rc.177 (#87)
2026-10-19 16:07:31 +02:00
CUDAWrapper.h
v1.0.0-rc.177 (#87)
2026-10-19 16:07:31 +02:00
DarkMaskSettings.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
DarkMaskSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DatasetSettings.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
DatasetSettings.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
Definitions.h
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
DetectorGeometry.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorGeometryFixed.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
DetectorGeometryFixed.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorGeometryModular.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
DetectorGeometryModular.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorModuleGeometry.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
DetectorModuleGeometry.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorModules.cpp
DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked
2026-10-21 09:41:35 +02:00
DetectorModules.h
DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked
2026-10-21 09:41:35 +02:00
DetectorOrientation.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DetectorOrientation.h
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DetectorSettings.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
DetectorSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
DetectorSetup.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
DetectorSetup.h
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
DetectorTransformation.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
DetectorTransformation.h
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
DiffractionExperiment.cpp
Merge branch 'panel-s4' into panel-s5
2026-10-21 11:27:51 +02:00
DiffractionExperiment.h
Serial XFEL stills inputs: readers from the files themselves, module geometry and its refinement
2026-10-20 23:30:48 +02:00
DiffractionGeometry.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
DiffractionGeometry.h
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiffractionSpot.cpp
Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table
2026-10-21 12:44:40 +02:00
DiffractionSpot.h
Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
2026-10-21 10:29:07 +02:00
FFTWPlannerLock.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
FileWriterSettings.cpp
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
FileWriterSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
GitInfo.cpp.in
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
GitInfo.h
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
GitInfoStamp.cmake
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
GoniometerAxis.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
GoniometerAxis.h
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
GridScanSettings.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
GridScanSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
Histogram.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
hkl_key.h
v1.0.0-rc.124 (#31)
2026-02-01 13:29:33 +01:00
HostMemory.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
HostMemory.h
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ImageBuffer.cpp
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ImageBuffer.h
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
ImageFormatSettings.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
ImageFormatSettings.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
IndexingSettings.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
IndexingSettings.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
InstrumentMetadata.cpp
version 1.0.0-rc.27
2024-12-02 21:17:14 +01:00
InstrumentMetadata.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
JFJochException.h
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
JFJochMath.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
JFJochMessages.h
writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does
2026-10-22 20:18:51 +02:00
JFJochReceiverPlots.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
JFJochReceiverPlots.h
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
JfjochTCP.h
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
Logger.cpp
broker: the journal keeps operational events; rugnux's processing log goes to it only when verbose
2026-10-19 22:12:07 +02:00
Logger.h
broker: the journal keeps operational events; rugnux's processing log goes to it only when verbose
2026-10-19 22:12:07 +02:00
ModuleShift.h
Serial XFEL stills inputs: readers from the files themselves, module geometry and its refinement
2026-10-20 23:30:48 +02:00
ModuleSummation.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
ModuleSummation.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
MovingAverage.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
MovingAverage.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
MtzTable.h
v1.0.0-rc.176 (#86)
2026-10-19 07:03:28 +02:00
MultiLinePlot.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
MultiLinePlot.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
NetworkAddressConvert.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
NetworkAddressConvert.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
PanelBoxes.cpp
Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
2026-10-21 10:29:07 +02:00
PanelBoxes.h
Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
2026-10-21 10:29:07 +02:00
PanelRows.h
Dense per-pixel maps through the panel table (panel layout stage 1)
2026-10-21 10:26:30 +02:00
ParallelFor.h
v1.0.0-rc.177 (#87)
2026-10-19 16:07:31 +02:00
PixelMask.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
PixelMask.h
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
Plot.h
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
print_license.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
RawToConvertedGeometry.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
RawToConvertedGeometryCore.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
Reflection.h
Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed
2026-10-22 17:27:44 +02:00
ResolutionShells.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
ResolutionShells.h
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ROIAzimuthal.cpp
v1.0.0-rc.170 (#80)
2026-09-16 18:17:46 +02:00
ROIAzimuthal.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIBox.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIBox.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROICircle.cpp
v1.0.0-rc.170 (#80)
2026-09-16 18:17:46 +02:00
ROICircle.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIDefinition.cpp
version 1.0.0-rc.29
2024-12-08 13:26:13 +01:00
ROIDefinition.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ROIElement.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIElement.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIMap.cpp
Dense per-pixel maps through the panel table (panel layout stage 1)
2026-10-21 10:26:30 +02:00
ROIMap.h
Dense per-pixel maps through the panel table (panel layout stage 1)
2026-10-21 10:26:30 +02:00
ScalingSettings.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
ScalingSettings.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
ScanResult.cpp
v1.0.0-rc.44
2025-06-15 17:46:46 +02:00
ScanResult.h
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
ScanResultGenerator.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
ScanResultGenerator.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
SpotToSave.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
SpotToSave.h
Panel id on spots and the panel table in the start message
2026-10-21 10:28:23 +02:00
StatusVector.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
StatusVector.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
TableChecksum.h
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
ThreadAffinity.cpp
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
ThreadAffinity.h
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
ThreadSafeFIFO.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
time_utc.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
TopPixels.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
TopPixels.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
UnitCell.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
UnitCell.h
v1.0.0-rc.175 (#85)
2026-10-16 15:34:43 +02:00
XrayFluorescenceSpectrum.cpp
v1.0.0-rc.81
2025-09-21 19:27:51 +02:00
XrayFluorescenceSpectrum.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ZeroCopyReturnValue.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
ZeroCopyReturnValue.h
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
ZMQWrappers.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
ZMQWrappers.h
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00