leonarski_fandClaude Opus 5.5 1ebb28e3ab Merge cytc-mr into rc175: molecular replacement decides an R-free tie between groups with as many copies on every reflection (paired, 3 standard errors), else UNDECIDED as before ...

Cytochrome C from its sequence-exact AlphaFold model now places in P 32 2 1; MR replay survey of 193
sets: UNDECIDED 7 -> 4, all three newly decided correctly, no wrong decision.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

2026-10-15 11:44:13 +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

cuFFT plans kept for the process and lent to one user at a time, output unchanged

2026-10-14 21:54:26 +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

Model validation: budget counts only what is really held; fewer extra engines

2026-10-15 09:56:15 +02:00

ModelValidation.h

Model validation: budget counts only what is really held; fewer extra engines

2026-10-15 09:56:15 +02:00

MolecularReplacement.cpp

Molecular replacement: an R-free tie between groups with as many copies decided on every reflection

2026-10-15 11:43:33 +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

cuFFT plans kept for the process and lent to one user at a time, output unchanged

2026-10-14 21:54:26 +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

Model validation: one GPU budget for all its parts, 80% of the card's total

2026-10-15 08:05:50 +02:00

RigidBodyGPU.cu

Merge cufft-cache into rc175: cuFFT plans reused within a rugnux run and destroyed when it ends, output unchanged

2026-10-14 22:12:53 +02:00

RigidBodyGPU.h

Model validation: one GPU budget for all its parts, 80% of the card's total

2026-10-15 08:05:50 +02:00

RigidBodyGPUEngine.h

GPU or CPU decided up front from the card's total memory, never from what is free

2026-10-14 21:28:38 +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