gemmi's table lists some groups a second time on another origin ("P 42 21 2a", "P 21212(a)",
"I 2 2 2a", "C 1 21 1"). SameRotationGroups kept them as separate candidates, so the true group tied
with itself in R-free and the choice came out UNDECIDED: five single-copy sets of the --af-model
survey (and one partial-model set) ended there. A group equal to one already listed up to an origin
shift on the twelfths is now left out.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
The ENANTIOMORPH hand check ran a whole ValidateAgainstModel on the placed model: model read and frame
probe, a rigid body, a 9-replicate null (~0.5 s of the ~0.6-0.9 s), sigma_A, three maps written. The
decision needs only --model's rule: the model fits its null (the MR choice has already required its
own null of the same construction) and the anomalous map at the model's atoms is not inverted.
ReadModelAnomalousMap (ModelValidation) computes F_calc and F_mask to the data's resolution (GPU engine
where there is one), carries them through the bulk solvent MR scored the placement with (the overall
scale and anisotropic B do not move phases), and reads the anomalous map with the same code as the
validation: its coefficient construction and its reading at the atoms are factored out of Validate
(anomalous_coefficients, read_anomalous_map) and used by both, so plain --model is unchanged.
Hand check 0.6/0.6/0.9 s -> 0.027/0.028/0.040 s on 11if/7ris/9zmu; same ADOPTED/VETOED on all seven
cases tried (the three demos, two anomalous lysozyme sets and their mirrored-detector runs), with the
scatterer means and deepest troughs within 0.1 sigma of the full validation's.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
- An MR ENANTIOMORPH decision is taken into the answer's label only as --model takes a model's
enantiomorph: ValidateAgainstModel runs on the placed model (in a scratch directory, removed after)
and its adopted_model_enantiomorph - fit over its null, anomalous map at the atoms not inverted -
decides; otherwise ENANTIOMORPH_VETOED. The hand-check numbers go to the MODEL PRIOR section.
- Rotation and translation functions on the GPU (MolecularReplacementGPU.cu): one block per
orientation for the rotation function; per orientation the copies, the bin weights, a gather of the
Crowther-Blow coefficients (CSR lists, fixed order, no atomics) and a cuFFT C2R, block-reduced
statistics finished on the host in a fixed order. The CPU path (FFTW) is unchanged in what it
computes; the orientation-independent part of the translation function (TranslationSetup) is now
built once per group on either path.
- Rescoring: a placement clashing with its mates over twice the limit is not refined, one rigid-body
engine per group, and the null is built only for the candidate the choice falls on.
Measured MR step on the RTX 5080 (before -> after, seconds; hand check extra where it runs):
3r6o 1.77 -> 0.67, neg 2.14 -> 0.37, 11if 1.20 -> 0.51 (+0.6 hand check), 7ris 1.46 -> 0.56 (+0.6),
9zmu 4.71 -> 1.07 (+0.9). Rotation 0.50 -> 0.02 s and translation 1.17 -> 0.13 s on 9zmu.
Mirrored-detector runs of two anomalous lysozyme sets: the hand check vetoes (map inverted at the
model's atoms); the unmirrored runs adopt.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
A predicted model (AlphaFold mmCIF, pLDDT in the B column) is trimmed at pLDDT 70, given B-factors
from the pLDDT (Oeffner et al. 2022) and placed by molecular replacement, one copy in the ASU:
- rotation function on a uniform 6 deg sampling of the point group's rotation ASU, each orientation
scored by the correlation of E^2 with the symmetry-summed |F|^2 read off the model's molecular
transform, computed once by FFT and interpolated (Navaza 1994);
- full-symmetry Crowther & Blow translation function (one FFT per orientation and group, through
MapFromFPhi/FFTW) for the 50 best orientations in every group with the merge's rotations;
- the best three placements per group through RefineRigidBody (GPU where there is one), bulk solvent
and R-free to 3 A, a C-alpha packing check against symmetry mates, Matthews, and the
random-orientation null for a placed candidate.
Decision: PLACED = TF Z >= 8, clash <= 5%, Vm in [1.5, 4), null >= 3 sd. Within the answer's merge
the placed group with the lowest R-free is chosen where it leads every other packing group by 0.03;
the twin hypothesis' merge is searched, and chosen, only where no group of the answer's merge can
hold the model at all (Matthews, packing). An enantiomorph relabels the answer as --model does;
another group goes to <prefix>_mr.mtz/.cif plus <prefix>_mr_model.pdb; the MODEL PRIOR report
section carries the table. The search runs on the CPU in both builds; without --af-model nothing
changes.
Measured (RTX 5080, MR step): 3r6o twin I41 chosen over I4122 (Matthews + clash) in 1.8 s, solution
0.09 A CA rmsd from Phaser's; 11if P41 -> P43 1.2 s; 7ris P3121 -> P3221 1.7 s; 9zmu P6122 -> P6522
4.7 s; 11if's model against 3r6o's data NOT_PLACED.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3
leonarski_fandClaude Opus 5.5