run lab6-fixed-opus-1
transcript /Users/yue/.claude/projects/-Users-yue-rietx-agent-runs-2026-10-01-wp1504-figure-work-lab6-fixed-opus-1/06c6d3b9-8b6b-424f-8e8e-26777c4cfeb7.jsonl

   #  offset    dur    chars     tool       head
   1     2.4    0.0       22     Skill      skill
   2     4.6    0.1     7339     Bash       cat .claude/skills/rietx/references/api-figure.md; ls; cat lab6.cif
   3     8.6    0.6     7418     Bash       P=../../venvs/fixed/bin/python; $P -c "
   4    15.7    0.6      114     Bash       ../../venvs/fixed/bin/python -c "
   5    24.8    0.8      292     Bash       cat > draw.py <<'EOF'
   6    27.8    0.0   433640     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/lab6-fixed-opus-1/figure.png
   7    32.2    0.8      245     Bash       sed -i '' 's/^g\["polyhedra"\] = \[\]/&\ng["sites"][0]["radius"] = 0.9/' draw.py && sed 
   8    35.1    0.0   366984     Read       /Users/yue/rietx-agent-runs/2026-10-01-wp1504-figure/work/lab6-fixed-opus-1/figure.png

8 tool calls (5 Bash, 2 Read, 1 Skill), 0 errored
9 API calls, 0.7 min wall, 0.28 M cache-read, 31 k cache-write, 3 k output, mean context 34 k
models: claude-opus-5-5 ×9

0 traced interpreter starts, 10 traced calls
refinement 0.0 s in 0 fit calls (0.0% of wall)
per-process floor 0.0 s of 2.4 s (0.0%)
    build                                 6      0.0 s [bond_tolerance, centres, disorder, ligands, max_atoms, probability]
    keep                                  2      0.0 s
    render_structure                      2      0.3 s [path, polyhedra, size, view, polyhedra=False, size=1000]
