leonarski_fandClaude Opus 5.5
234774ff09
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battery.py timing --benchmark standard (now the default) runs 9zlo, 9s02 and
9gjx from their AlphaFold DB models (AF-P17090-F1, AF-P32322-F1, AF-Q65MG6-F1
v6, with their PAE, as the 2026-10-16 AlphaFold MR scan used them; all three
GREEN there) and 4nwv from its deposited model moved by the existing fixed
transform. --benchmark inhouse keeps the earlier myob_x10sa / cytc_x10sa /
4nwv list. Same checks; expected groups are the deposited ones, R-free <= 0.50
for the predictions (0.35 for 4nwv), placement CC >= 0.30.
So that a machine needs only the raw data:
- the deposited coordinates of 9zlo, 9s02, 9gjx, 4nwv and 4dc8 (the inhouse
myoglobin reference) are committed in tools/battery/models/pdb/ as the
compressed mmCIF RCSB serves (CC0; 50-660 kB each, 1.6 MB together), and
model_check.deposition reads an entry there before the pdb_cache, taking
its refinement record from the file itself - no cache JSON, no network;
- open/inhouse arms default their manifest and reference, so a site config
is just runs_root plus the data roots (site.timing.example.json);
- baseline_timing is now per benchmark ({"standard": RUN, "inhouse": RUN}).
Verified on the workstation through the GPU lock with a site config whose
pdb_cache is an empty directory (still empty afterwards): standard 4/4 pass
(9zlo 19 s, 9s02 30 s, 9gjx 21 s, 4nwv 89 s), inhouse 3/3 pass.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4
