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leonarski_fandClaude Opus 5.5 30c7bee15f rugnux: --af-model becomes --mr, for predictions and experimental structures alike 
- The option is --mr <file>. What kind of model it is is read from the file: a prediction where it
  is ModelCIF (_ma_qa_metric) or has no cell and one B value per residue in 0-100 (AlphaFold PDB/mmCIF);
  an experimental structure otherwise. A prediction is handled as before (pLDDT >= 70 trim, B from
  pLDDT, PAE domains where the AlphaFold DB's PAE file sits beside it). An experimental structure is
  taken as its polymer - no waters, ligands, hydrogens or alternative conformers, occupancy 1, isotropic
  B as refined - with a coordinate error of 0.67 A (a prediction's at pLDDT 90) for sigma_A; a B column
  above 100 no longer stops the search.
- The report section is MOLECULAR REPLACEMENT (EXPERIMENTAL), its keys MR_* (MR, MR_MODEL_FILE,
  MR_MODEL_KIND, MR_DECISION, MR_SPACE_GROUP, MR_COPIES, MR_HAND_CHECK, MR_SECONDS, ...); the <prefix>_mr
  outputs are unchanged.
- The twin hypothesis' merge that is made only for the model to test (a metric re-ask promoted the
  indexed lattice's group) is written and reported only where the model chooses the subgroup.

Raw deposited coordinates of nine control sets, unconverted: every one placed and confirmed against the
deposition (all chains as one body), the groups the same as with the prediction or the prepared model.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3
2026-10-12 19:30:22 +02:00
..
crystfel
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
data
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
test_data
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
xds
XDS plugin 1.1.0: mask module/chip edges, pass saturation through; recommend Durin
2026-10-08 10:56:34 +02:00
xds_durin
XDS plugin 1.1.0: mask module/chip edges, pass saturation through; recommend Durin
2026-10-08 10:56:34 +02:00
xds_neggia
XDS plugin 1.1.0: mask module/chip edges, pass saturation through; recommend Durin
2026-10-08 10:56:34 +02:00
AcquisitionCountersTest.cpp
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
AdaptiveSpotFinderCPUTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
AdaptiveSpotFinderGPUTest.cpp
GPU azimuthal profile: sum the corrected values in fixed point
2026-10-08 12:33:34 +02:00
AdaptiveThresholdTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
AnisotropyAnalysisTest.cpp
Anisotropy verdict: the directional limits are a second hypothesis beside the tensor
2026-10-11 02:21:32 +02:00
AutoIncrVectorTest.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
AzimuthalIntegrationTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
BackgroundGainTest.cpp
rugnux: background clip scaled by the CCD gain measured in the pre-scan
2026-10-09 21:18:12 +02:00
BandwidthEstimateTest.cpp
Move SpotWidth to bragg_integration/, SpindleCuspLoss and LeftoverLattices to indexing/
2026-10-07 14:05:37 +02:00
BeamCenterFFTGPUTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
BeamCenterFFTTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
BeamCenterFromBackgroundTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BearerTokensTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
BraggIntegrationEngineCompressedImageTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BraggIntegrationEngineCPUTest.cpp
rugnux two-pass: the integration radius decided on the pre-pass frames, before the canonical pass
2026-10-11 13:01:23 +02:00
BraggIntegrationEngineGPUTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BraggStencilTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
BrokerHttpAuthTest.cpp
Broker: a collection can be followed from /start, its start message comes in the event stream
2026-10-08 17:03:09 +02:00
BSLZ4DecoderGPUFuzzTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
BSLZ4DecoderGPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
CalcBraggPredictionTest.cpp
BraggPredictionRot: walk only the l of each column that can pass the phi test
2026-10-08 06:46:28 +02:00
CalibrationTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CBORTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
CCTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
CheckImageOutput.h
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
CMakeLists.txt
rugnux --af-model (experimental): single-copy molecular replacement of a predicted model
2026-10-11 13:35:05 +02:00
CoordTest.cpp
v1.0.0-rc.41
2025-06-10 18:14:04 +02:00
CorrectionSurfaceGPUTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
CrystalLatticeTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
CrystalSettingTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
CudaHandledErrorTest.cpp
Indexer failures are thrown, not read as "no lattice"; GPU memory errors say what to do
2026-10-10 18:56:00 +02:00
CUDAMemHelpersTest.cpp
tests: FFT-indexer admission test fills every card, right before each Run
2026-10-11 16:39:43 +02:00
DectrisSimplonClientTest.cpp
DectrisSimplonClient: separate connections for commands and status reads
2026-10-08 22:53:01 +02:00
DetectorGeometryTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
DetectorSettingsTest.cpp
v1.0.0-rc.139 (#49)
2026-04-29 09:50:50 +02:00
DetectorSetupTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
DetGeomCalibTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiagnosticOutputTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
DiffractionExperimentTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiffractionGeometryTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
DiffractionSpotTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
enospc_shim.c
SHIM library improvements from the HDF Group
2026-05-08 11:39:51 +02:00
FPGAFrameGeneratorTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
FPGAHLSModulesTest.cpp
v1.0.0-rc.91
2025-10-20 20:43:44 +02:00
FPGAHostWriterTest.cpp
v1.0.0-rc.34
2025-04-14 11:52:06 +02:00
FPGAIntegrationTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
FPGANetworkTest.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
FPGAPTPTest.cpp
v1.0.0-rc.72
2025-09-08 20:28:59 +02:00
FPGASpotFindingUnitTest.cpp
v.1.0.0-rc.32
2025-03-24 12:16:33 +01:00
FrameTransformationTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
FrenchWilsonTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
GoniometerAxisTest.cpp
v1.0.0-rc49
2025-06-18 15:19:18 +02:00
GridScanSettingsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
HDF5WritingTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
HistogramTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
HKLKeyTest.cpp
v1.0.0-rc.124 (#31)
2026-02-01 13:29:33 +01:00
HotPixelFinderTest.cpp
rugnux pre-scan: projection and defective pixels per card, the sample read once, beam stop memoised
2026-10-12 08:11:05 +02:00
ImageBufferTest.cpp
v1.0.0-rc.128 (#35)
2026-03-03 22:24:44 +01:00
ImageMetadataTest.cpp
v1.0.0-rc.103 (#8)
2025-11-19 09:40:50 +01:00
ImagePreprocessorGPUFusedTest.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
ImageSpotFinderCPUTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
ImageSpotFinderGPUTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
IndexingUnitTest.cpp
rugnux: doubled-cell hypothesis - the supercell probe reads its class to the limit, and a class that stands clear is merged in the doubled cell as well
2026-10-10 10:47:55 +02:00
JFCalibrationTest.cpp
v1.0.0-rc.36
2025-05-05 19:32:22 +02:00
JFConversionTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
jfjoch_hdf5_enospc_test.cpp
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
JFJochReaderTest.cpp
HDF5 reader: read variable-length string attributes and datasets
2026-10-09 21:15:01 +02:00
JFJochReceiverIntegrationTest.cpp
v1.0.0-rc.150 (#60)
2026-06-15 20:24:15 +02:00
JFJochReceiverLiteTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
JFJochReceiverPlotsTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
JFJochReceiverProcessingTest.cpp
v1.0.0-rc.160 (#70)
2026-07-19 09:39:28 +02:00
JFJochStateMachineTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
JFPedestalTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
JPEGTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LatticeReductionTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
LatticeSearchTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LePageLatticeTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
LiveCollectionTest.cpp
Broker: a collection can be followed from /start, its start message comes in the event stream
2026-10-08 17:03:09 +02:00
LoadReferenceMtzFreeFlagsTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LoadReferenceSfCifTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
LossyFilterTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
MergeScaleTest.cpp
Global Wilson B: minimum fit window, no upper cap
2026-10-11 02:21:32 +02:00
ModelMaskGPUTest.cpp
ModelMaskGPU: gemmi's shrink step, so fine rigid-body zones stay on the GPU
2026-10-09 12:38:37 +02:00
ModelScaleGPUTest.cpp
Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/
2026-10-07 14:05:37 +02:00
ModelScalingTest.cpp
--model: the bulk-solvent b_sol ceiling follows the model's atomic B
2026-10-10 20:47:04 +02:00
ModelValidationTest.cpp
rugnux --model: a wrong model confirms no shell, fits no hand, and fits the GPU reserve
2026-10-11 21:30:34 +02:00
ModuleSummationTest.cpp
version 1.0.0-rc.27 minor fixes
2024-12-04 20:58:51 +01:00
MolecularReplacementTest.cpp
rugnux: --af-model becomes --mr, for predictions and experimental structures alike
2026-10-12 19:30:22 +02:00
MovingAverageTest.cpp
v1.0.0-rc.31
2025-03-02 13:15:28 +01:00
MultiLatticeSearchTest.cpp
v1.0.0-rc.148 (#58)
2026-06-08 08:30:35 +02:00
nxmx_geometry_dials_test.py
v1.0.0.rc-162 (#72)
2026-08-25 08:21:39 +02:00
PairSortGPUTest.cpp
RotationScaleMerge: sort the outlier band's log-spread pairs on the device
2026-10-08 07:27:25 +02:00
ParallelForTest.cpp
rugnux: on a machine of several sockets, keep to the sockets the GPUs are on
2026-10-11 09:27:32 +02:00
PedestalCalcTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
PixelMaskTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
PortableTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
PostRefineTest.cpp
rugnux hypothesis arms read their residual on the pre-pass frames
2026-10-11 07:12:05 +02:00
PreflightTest.cpp
v1.0.0-rc.165 (#75)
2026-08-27 22:16:54 +02:00
PreviewCounterTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
RawToConvertedGeometryTest.cpp
v1.0.0-rc.97
2025-11-09 12:42:27 +01:00
RegressionTest.cpp
1.0.0-rc.89
2025-10-01 22:54:40 +02:00
ReindexAmbiguityTest.cpp
Model validation expands strict NCS; the written cell follows the model's indexing
2026-10-10 13:35:49 +02:00
ResolutionShellsTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ResultReportTest.cpp
rugnux --model: a wrong model confirms no shell, fits no hand, and fits the GPU reserve
2026-10-11 21:30:34 +02:00
RfreeFlagsTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
RingsFromProfileTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
ROIIntegrationCPUTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIIntegrationGPUTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ROIMapTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
RotationIndexerTest.cpp
Indexer failures are thrown, not read as "no lattice"; GPU memory errors say what to do
2026-10-10 18:56:00 +02:00
RotationScaleWalkTest.cpp
rugnux: the no-crystal near-tie line prints the exact log10 tail against log10 significance
2026-10-10 09:33:34 +02:00
RugnuxLargeTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
RugnuxTest.cpp
Merge branch 'doubled-cell' into rc175: a doubled-cell hypothesis for a half-translation pseudo-symmetry that breaks down with resolution
2026-10-10 15:18:14 +02:00
SearchSpaceGroupTest.cpp
SearchSpaceGroup: offer every monoclinic setting the holohedry holds; break sibling ties on axial screw evidence
2026-10-09 21:42:33 +02:00
SearchSpaceGroupTwinTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
ShadowFinderTest.cpp
rugnux pre-scan: projection and defective pixels per card, the sample read once, beam stop memoised
2026-10-12 08:11:05 +02:00
SphericalHarmonicSurfaceTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
SpindleBlindFractionTest.cpp
v1.0.0-rc.167 (#77)
2026-09-09 07:25:13 +02:00
SpindleCuspLossTest.cpp
Move SpotWidth to bragg_integration/, SpindleCuspLoss and LeftoverLattices to indexing/
2026-10-07 14:05:37 +02:00
SpotExtractorGPUParityTest.cpp
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
SpotFootprintTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
SpotUtilsTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
StatusVectorTest.cpp
v1.0.0-rc.127 (#34)
2026-03-02 15:57:12 +01:00
StreamWriterTest.cpp
Writer and broker: the master file appears only after every data file it links to
2026-10-08 14:55:56 +02:00
StrongPixelSetTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
SweepLayoutTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00
SyntheticMergedReflections.h
v1.0.0.rc-161 (#71)
2026-08-13 17:03:10 +02:00
TCPImagePusherTest.cpp
TCP pusher: never block the receiver thread; queue bounded by image-buffer slots
2026-10-10 21:11:09 +02:00
TestData.h
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
ThreadSafeFIFOSetTest.cpp
v1.0.0-rc.135 (#44)
2026-04-16 11:59:59 +02:00
TIFFTest.cpp
v1.0.0-rc.153 (#63)
2026-06-23 20:29:49 +02:00
TimeTest.cpp
v1.0.0-rc.96 (#1)
2025-11-02 13:45:57 +01:00
TopPixelsTest.cpp
v1.0.0-rc.121 (#28)
2025-12-12 21:24:20 +01:00
TranslationalNCSTest.cpp
v1.0.0-rc.172 (#82)
2026-09-22 06:48:37 +02:00
TwinningAnalysisTest.cpp
rugnux: write the twin hypothesis beside the answer as <prefix>_twin_<SG>.mtz/.cif
2026-10-09 19:40:22 +02:00
UnitCellTest.cpp
v1.0.0-rc.146 (#56)
2026-05-28 18:48:35 +02:00
WilsonOutliersTest.cpp
RotationScaleMerge: the Wilson outlier test on the device in the GPU build
2026-10-08 07:07:32 +02:00
WriteReflectionsTest.cpp
Merged mmCIF: drop the scaled unmerged block
2026-10-09 18:51:56 +02:00
XDSPluginTest.cpp
XDSPluginTest: expect a signed image's INTx_MAX to pass through as saturated
2026-10-08 12:36:40 +02:00
XtalOptimizerTest.cpp
v1.0.0-rc.166 (#76)
2026-09-02 21:17:31 +02:00
XtalRefineCeres.h
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
XtalRefineTest.cpp
1.0.0-rc.174 (#84)
2026-10-06 14:03:18 +02:00
ZMQImagePusherTest.cpp
v1.0.0-rc.169 (#79)
2026-09-15 17:09:31 +02:00
ZMQMetadataSocketTest.cpp
v1.0.0-rc.133
2026-03-26 20:50:33 +01:00
ZMQPreviewSocketTest.cpp
version 1.0.0-rc.25
2024-11-22 21:25:20 +01:00
ZSTDCompressorTest.cpp
v1.0.0-rc.173 (#83)
2026-09-29 15:57:32 +02:00