leonarski_fandClaude Opus 5.5
f99ed0b5ac
`battery.py timing --rugnux BIN` runs myob_x10sa and cytc_x10sa from their AlphaFold DB predictions (AF-P68082-F1 and AF-P62894-F1, v6, committed verbatim with their predicted aligned error under tools/battery/models/, CC BY 4.0) and 4nwv from its deposited model with strict NCS expanded and moved by a fixed rigid-body transform (30 deg about (0.36, 0.48, 0.80) through the centroid, shift (12, -18, 25) A), made at run time from the site's pdb_cache. Each set runs the battery's own command for its arm, in an ordinary run directory, so the site config, results.json, report, table and compare all apply. A set passes when the battery's own verdict passes, MODEL_PLACEMENT is MR, MR_SPACE_GROUP is the expected group with its hand, R_FREE is under its limit, CC_MODEL_CONFIRMED_TO_D_MIN is not NONE, and the placed model's intensities correlate with the reference model's (|F|^2, shell-normalised, 10-4 A, best over the lattices' changes of basis) at 0.30 or more. That last check is independent of rugnux's scores: correct placements give 0.55 / 0.90 / 0.96; the myoglobin placement turned by 30 deg with rugnux's report unchanged gives 0.035, the unplaced 4nwv start model 0.011, a placement relabelled to the other hand 0.18. Rows carry the checks and the per-step times from the TIMING step lines; the report gets a Timing benchmark section; the run exits 1 on any failure. On the workstation (RTX 5080, rc175 8eacce): myoglobin passes in 10 s (R-free 0.44), 4nwv in 106 s (MR 34 s, R-free 0.315 against 0.297 for the deposited placement). Cytochrome c fails: MR places three copies of the monomer in both P 32 2 1 and P 31 2 1 within 0.03 in R-free and so places neither (MR_DECISION UNDECIDED), where the three-copy reference model decides the hand at once. battery.py now imports fcntl only for the full-run lock, falls back to Popen.kill where there are no process groups, and keeps the binary's extension in the run directory, so a timing run can work on Windows (untried there). Licence and credit: licenses/alphafold-db.txt (from models/LICENSE.txt via COLLECT.sh), a new "Data files in the repository" table in THIRD_PARTY_NOTICES.md, and the AlphaFold DB with Jumper et al. 2021 and Varadi et al. 2022 and 2024 in docs/ACKNOWLEDGEMENT.md. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
18 lines
2.3 KiB
JSON
18 lines
2.3 KiB
JSON
{
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"about": "Timing benchmark (README: 'The timing benchmark'): three sets, each started from a model rugnux has to place by molecular replacement, timed per step and checked for a right answer. 'start' is the model given to --model: an AlphaFold DB prediction committed in models/ (with its predicted aligned error beside it), or a deposited entry from the site's pdb_cache moved by a fixed rigid-body transform (strict NCS expanded first, then x' = R (x - c) + c + t, R a rotation by 'deg' about the unit 'axis', c the centroid of the expanded asymmetric unit, t 'shift' in A). The reference model the placement is checked against is the one the battery itself uses for the set (its manifest row's 'model', else the PDB entry of the set id). 'expect': 'mr_sgno' the space group the placed model is in (the model decides the hand), 'rfree_max' the highest R_FREE accepted, 'cc_min' the lowest correlation of the placed model's intensities with the reference model's (shell-normalised, 10-4 A, best over the lattice's reindexing operators).",
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"sets": [
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{"set": "myob_x10sa", "arm": "inhouse",
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"start": {"alphafold": "models/AF-P68082-F1-model_v6.cif",
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"why": "AlphaFold DB AF-P68082-F1 v6: myoglobin, Equus caballus (UniProt P68082), the species of the battery's reference model 4DC8 (horse heart). No heme"},
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"expect": {"mr_sgno": 4, "rfree_max": 0.50, "cc_min": 0.30}},
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{"set": "cytc_x10sa", "arm": "inhouse",
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"start": {"alphafold": "models/AF-P62894-F1-model_v6.cif",
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"why": "AlphaFold DB AF-P62894-F1 v6: cytochrome c, Bos taurus (UniProt P62894), the protein of the battery's reference model (bovine heart, placed with 6FF5). No heme; three copies to place, related by a pseudo-translation"},
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"expect": {"mr_sgno": 154, "rfree_max": 0.50, "cc_min": 0.30}},
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{"set": "4nwv", "arm": "open",
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"start": {"moved": {"pdb": "4nwv", "axis": [0.36, 0.48, 0.80], "deg": 30.0, "shift": [12.0, -18.0, 25.0]},
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"why": "the deposited model of 4NWV (I222, a virus capsid: 3 chains and 14 strict NCS operators, 45 chains once expanded), turned 30 deg and shifted 33 A: far outside what the rigid body corrects, so it is rejected and molecular replacement places the whole asymmetric unit"},
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"expect": {"mr_sgno": 23, "rfree_max": 0.35, "cc_min": 0.30}}
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]
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}
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