leonarski_fandClaude Opus 5.5 402b3d1293 ACKNOWLEDGEMENT: autoPROC and Clemens Vonrhein; DOIs verified; DISTL; tNCS credit in MR ...

- All 84 DOIs checked (82 on Crossref, 2 DataCite): title, journal, volume, pages and first author
  match; Matthews 1968 and Yeates 1997 links percent-encode their parentheses; the MOSFLM link
  points at a page that answers.
- autoPROC: an explicit acknowledgement of Clemens Vonrhein (Global Phasing) for the principle that a
  pipeline should verify the metadata it is given - beam centre, geometry, goniometer - and correct
  it where it is wrong; Vonrhein et al. (2011) Acta Cryst. D67, 293-302 (DOI checked).
- Zhang, Sauter et al. (2006) DISTL, already credited in SpotFindingSettings.h, gets its entry.
- Molecular replacement: tNCS looked for in the native Patterson as Read, Adams & McCoy do; the same
  credit at DetectTranslationalNcs (comment only).

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3

2026-10-13 09:03:32 +02:00

..

CMakeLists.txt

rugnux --af-model: anomalous veto on the enantiomorph, search on the GPU, cheaper rescoring

2026-10-11 17:10:48 +02:00

ModelDensityGPU.cu

rugnux: model validation's structure factors and maps on the GPU

2026-10-09 12:38:37 +02:00

ModelDensityGPU.h

rugnux: model validation's structure factors and maps on the GPU

2026-10-09 12:38:37 +02:00

ModelFFT.cpp

Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

2026-10-07 14:05:37 +02:00

ModelFFT.h

Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

2026-10-07 14:05:37 +02:00

ModelGrid.cpp

ModelGrid: an atom's points within its radius are gathered, then gridded in one vectorised pass

2026-10-10 10:47:27 +02:00

ModelGrid.h

Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

2026-10-07 14:05:37 +02:00

ModelMaskGPU.cu

ModelMaskGPU: gemmi's shrink step, so fine rigid-body zones stay on the GPU

2026-10-09 12:38:37 +02:00

ModelMaskGPU.h

ModelMaskGPU: gemmi's shrink step, so fine rigid-body zones stay on the GPU

2026-10-09 12:38:37 +02:00

ModelScaleGPU.cu

--model: the bulk-solvent b_sol ceiling follows the model's atomic B

2026-10-10 20:47:04 +02:00

ModelScaleGPU.h

--model: the bulk-solvent b_sol ceiling follows the model's atomic B

2026-10-10 20:47:04 +02:00

ModelScaling.cpp

Model validation: scale fits on the GPU, change-of-basis probe gridded once per frame on all threads

2026-10-12 21:40:54 +02:00

ModelScaling.h

Model validation: scale fits on the GPU, change-of-basis probe gridded once per frame on all threads

2026-10-12 21:40:54 +02:00

ModelStructureFactorsGPU.cpp

Merge branch 'modelpar' into gpusf

2026-10-09 13:51:41 +02:00

ModelStructureFactorsGPU.cu

rugnux: model validation's structure factors and maps on the GPU

2026-10-09 12:38:37 +02:00

ModelStructureFactorsGPU.h

rugnux --af-model: molecular replacement faster - the score's scale fit on the GPU, the expected LLG gate, the serial parts side by side

2026-10-12 16:39:03 +02:00

ModelStructureFactorsGPUEngine.h

rugnux: model validation's structure factors and maps on the GPU

2026-10-09 12:38:37 +02:00

ModelValidation.cpp

docs: bring the rugnux and analysis pages up to the code (MR fallback, GPU decode, live runs)

2026-10-13 09:03:31 +02:00

ModelValidation.h

rugnux --model: molecular replacement where the rigid body does not place the model

2026-10-12 22:20:36 +02:00

MolecularReplacement.cpp

ACKNOWLEDGEMENT: autoPROC and Clemens Vonrhein; DOIs verified; DISTL; tNCS credit in MR

2026-10-13 09:03:32 +02:00

MolecularReplacement.h

rugnux: --af-model becomes --mr, for predictions and experimental structures alike

2026-10-12 19:30:22 +02:00

MolecularReplacementGPU.cu

rugnux --af-model: the further copies' translation function prepared once per group, the known copies' likelihood beside it

2026-10-12 19:30:22 +02:00

MolecularReplacementGPU.h

rugnux --af-model: the further copies' translation function prepared once per group, the known copies' likelihood beside it

2026-10-12 19:30:22 +02:00

RigidBodyGPU.cpp

RefineRigidBody: a body refined beside fixed copies of it

2026-10-12 00:26:49 +02:00

RigidBodyGPU.cu

RefineRigidBody: a body refined beside fixed copies of it

2026-10-12 00:26:49 +02:00

RigidBodyGPU.h

Merge branch 'modelpar' into gpusf

2026-10-09 13:51:41 +02:00

RigidBodyGPUEngine.h

RefineRigidBody: a body refined beside fixed copies of it

2026-10-12 00:26:49 +02:00

RigidBodyRefine.cpp

RefineRigidBody: a body refined beside fixed copies of it

2026-10-12 00:26:49 +02:00

RigidBodyRefine.h

RefineRigidBody: a body refined beside fixed copies of it

2026-10-12 00:26:49 +02:00

SigmaA.cpp

Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

2026-10-07 14:05:37 +02:00

SigmaA.h

Move the atomic-model code to image_analysis/structure_refinement/ and WriteModel to writer/

2026-10-07 14:05:37 +02:00