`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>
leonarski_fandClaude Opus 5.5
f99ed0b5ac