dfd69fcb9172229eaabefd1897c9e23d07caaca2
8
Commits
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  leonarski_fandClaude Opus 5.5
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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 |
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leonarski_fandClaude Opus 5.5
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6c8ead466a |
rugnux --af-model: molecular replacement faster - the score's scale fit on the GPU, the expected LLG gate, the serial parts side by side
The search was CPU-bound: on a 54-chain partial complex ~80% of all CPU samples were the score's FitModelScale grid (and libm's exp under it), with the GPU busy 13 of 37 s. - score_placement fits its scale on the GPU where its structure factors are made there (ModelScaleGPU's FitSolvent / Fit, as the rigid body already does); equal to rounding, the CPU build unchanged. - A model whose expected log-likelihood gain (sum sigma_A^4 / 2, McCoy et al. 2017; sigma_A^2 the part of the scattering one copy is by Matthews, times Luzzati's D^2) is below 10 is not searched for. Over the 193-set survey the lowest eLLG of a placed model is 26; every PAE domain below 24 placed nowhere, so no decision changes. - The likelihood setups made where first needed, one serving both where the reflections are the same. - After a candidate fails its null, the other placed candidates' nulls side by side. - The first copy's placements refined side by side on an engine each; the groups' translation functions side by side; CopyFactors and KnownStructureFactors over threads; the further copies' CopyFactors and gains for the peaks walked all at once; the known-structure TF setup made while the first copy is refined. All exact. Survey replay (193 sets): no decision changes; two R values differ in the 3rd decimal (GPU scale). Alternating runs, MODEL_PRIOR_SECONDS base -> new: 54-chain complex 38.3 -> 14.7, 4mtk 18.3 -> 9.7, 9v16 13.7 -> 8.3 (shared machine, indicative). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3 |
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leonarski_fandClaude Opus 5.5
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0d33d7a40a |
rugnux --af-model: likelihood judging, PAE domains, twin comparison, tNCS carry test, faster multi-copy search
- Likelihood (Read 2001; Z-score over random positions as McCoy et al. 2005): log-likelihood gain of Rice/Woolfson E distributions, sigma_A from the pLDDT coordinate error with its scale refined, to 2.5 A (or the 20000 lowest-resolution reflections). Further-copy TF peaks ranked by the gain on the search's reflections (peaks that lower it dropped); a copy whose TF Z is below 8 also stands out where its refined likelihood Z-score reaches 8 - only where the copies placed are as many as Matthews makes most likely. The likelihood is computed only where a translation function does not stand out. Copy structure factors exact from one FFT of the cell's grid, or read off the molecular transform where it reaches the likelihood's resolution. - PAE domains: the AlphaFold DB's predicted_aligned_error JSON beside the model (same name pattern) is read automatically; average linkage on the symmetrised PAE (10 A, domains >= 40 residues). Where the whole model is placed nowhere, each domain is searched by itself side by side; placed domains must agree, and a domain alone may only confirm the answer's group. - Twin comparison: where the answer's merge chose and the twin hypothesis' merge exists, the chosen placement read as a crystal in the subgroup (its symmetry images as copies, the subgroup's setting found from the two cells) against the model searched for afresh in the subgroup, both against the data twinned by the law (fraction refined on the working set, Yeates 1997); the subgroup is taken by a 0.03 R-free lead plus its own null/margin -> TWIN_SUBGROUP, written to p_mr with law and fraction. With --af-model rugnux makes the subgroup merge wherever a metric re-ask promoted the indexed group. - tNCS rule: a group with fewer copies beside tNCS (screws bridged by the vector, or the enantiomorph) no longer leaves the choice undecided where the chosen copies, carried into it and refined, fit worse by 0.03 in R-free. - Speed: the molecular transform's FFT on the GPU (cuFFT, serialised), no rigid body for trials that lower the likelihood, re-search only with tNCS, PAE domains searched in parallel. Survey (193 sets, MR replay on stored merges): single GREEN 58 -> 68, multi 48 -> 58, partial 8 -> 9; 4bwl (and, in full runs, 2wnq and a withdrawn entry of the same protein) TWIN_SUBGROUP P21 instead of a wrong AGREES; a P21212 set with tNCS now SPACE_GROUP P21212 instead of UNDECIDED; no wrong call. CPU and GPU builds make the same decisions on 18 demo/multi-copy/twin sets. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3 |
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leonarski_fandClaude Opus 5.5
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63e0a85467 |
rugnux --af-model: several copies in the asymmetric unit, tNCS, a search-matched null, faster
Copy number. The hard "Vm >= 4: MULTI_COPY, no decision" rule is gone. Copies are searched one after another up to the largest copy number with a Matthews probability of 1% (a Gumbel distribution with Kantardjieff & Rupp's 2003 mode and mean, no resolution dependence); COPIES_LIKELY reports the most probable. Sequential search. Copy n's translation function carries copies 1..n-1 as a known partial structure: the cross term 2 Re(conj(F_known) F(t)) goes on the same FFT grid (CPU FFTW and GPU cuFFT; KnownStructureFactors, AssemblyCorrelation). Its peaks, past those that clash, are ranked by the correlation of the whole assembly with E^2 (the TF itself, linear in |F|^2, rewards copying a placed copy onto an origin shift), the first that stands out (TF Z >= 8), packs and lowers R-free by 0.01 is kept; each copy is refined beside the others held fixed (RefineRigidBody's fixed copies), and the first copy again beside the second, the earlier ones once more at the end. Packing: ClashFraction counts C-alpha clashes with other copies and all their mates, binned (7mzt: 51 s of clash checks -> 1.9 s). Search quality: rotation-function peaks hill-climbed off the 6 deg sampling (6ze4: RF Z 10.4 -> 16.0, 3.3 deg off the deposited orientation -> 0.2); the first copy goes down the TF list until three placements that pack are refined, so a group is CLASH only where no offered orientation packs; groups are searched side by side, and every group the best one leads is searched again with the best one's copy orientations tried first, the better search kept. tNCS: the native Patterson of E^2 (5-10 A) off the lattice; placed copies' orientations join every further copy's search; and where the tNCS vector turns one group's screw axes into another's (TncsRelatesGroups), a group whose search stopped at fewer copies does not lose to the other - UNDECIDED. Measured on an in-house tNCS crystal (vector c/3 along the 3-fold): both hands fit with three copies to within 0.01 in R-free, and where one hand's search failed the other was taken as ENANTIOMORPH; now UNDECIDED. Null: the replicates are placed by the translation function in their own orientation, as the search placed the real one (a null at the real centroid reads high), and the gate is 4.51 = t(8) sqrt(1 + 1/9), 3 sd of a nine-draw null, the gate --model's MODEL_FIT is now read at. Speed: placements scored on the GPU structure-factor engines; further copies' trials score with the first copy's bulk solvent held, the assembly refitted at the end. Survey of 193 sets (jfjoch_mr_replay on stored merges, RTX 5080 shared with other jobs): MR median 1.15 s, max 24 s; demos 0.8-1.1 s. Report: COPIES and COPIES_LIKELY columns, MODEL_PRIOR_COPIES. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3 |
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leonarski_fandClaude Opus 5.5
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f800669839 |
jfjoch_mr_replay: --af-model's molecular replacement re-run on a run's merged MTZ files
A developer utility, not installed: the search, the decision and the hand check run on the answer's p.mtz (and the twin hypothesis' p_twin_<group>.mtz) that a rugnux run wrote, so a survey of the search over every dataset with a predicted model takes minutes instead of a reprocessing per set. The hand check of an ENANTIOMORPH decision moves from the rugnux driver into CheckEnantiomorphHand, which both call; unchanged. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3 |
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leonarski_fandClaude Opus 5.5
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50e3b59fb7 |
rugnux --af-model: hand check reads only the anomalous map, on MR's placement and solvent
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> |
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leonarski_fandClaude Opus 5.5
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2a3d60fb82 |
rugnux --af-model: anomalous veto on the enantiomorph, search on the GPU, cheaper rescoring
- 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> |
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leonarski_fandClaude Opus 5.5
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60a8bf3981 |
rugnux --af-model (experimental): single-copy molecular replacement of a predicted model
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 |