STRC long-running jobs — bundle 2026-04-22
Two computations to run on Egor’s machine in tmux while Holt-blocked Mini-STRC waits.
What’s in here
| File | What it does | Wall-clock |
|---|---|---|
0-setup.sh | Creates strc-mmgbsa conda env, installs cas-offinder, downloads hg38 chr15 (PE off-target needs it) | 15-25 min |
1-run-phase4f.sh | Launches Phase 4f (interface ΔΔG via OpenMM single-point energies on Ultra-Mini × TMEM145 with top-3 leads pre-bound) in tmux | starts immediately, runs ~2-6 h |
2-run-pe-offtarget.sh | Launches Cas-OFFinder off-target scan on the maternal-allele pegRNAs from pe_phase3_allele_discrimination.json | starts immediately, runs ~10-30 min |
monitor.sh | tail -f both job logs side-by-side | manual |
pharmacochaperone_phase4f_interface_rescue.py | Real Phase 4f implementation (OpenMM + OpenFF-Toolkit). Replaces the scaffold in ~/Brain/research/strc/models/. | — |
pe_phase4_cas_offinder.py | New script: reads PE Phase 3 leads, runs cas-offinder against hg38 chr15, gates on off-target count | — |
Run order
cd ~/Desktop/strc-jobs-2026-04-22
# One-time setup (long install)
bash 0-setup.sh
# Then launch both jobs in detached tmux sessions
bash 1-run-phase4f.sh
bash 2-run-pe-offtarget.sh
# Watch progress whenever
bash monitor.shSessions created
| tmux session | What | Log file |
|---|---|---|
phase4f | Pharmacochaperone interface-rescue | ~/Brain/research/strc/logs/phase4f-<timestamp>.log |
pe-offtarget | PE off-target Cas-OFFinder | ~/Brain/research/strc/logs/pe-offtarget-<timestamp>.log |
tmux ls, tmux attach -t phase4f, Ctrl-b d to detach, tmux kill-session -t phase4f to abort.
Method honesty
- Phase 4f uses OpenMM single-point energies with implicit GB (GBn2), not full MM-GBSA from MD trajectories. This is a static-snapshot approximation: cheaper, faster, ~1-2 kcal/mol noisier than dynamic MM-GBSA. If the result is unambiguous (clear pass or clear fail), it’s enough. If margin is within ±2 kcal/mol of the 30% gate, we’ll need a follow-up Phase 5 short MD + dynamic MM-GBSA on the top hit.
- PE off-target uses Cas-OFFinder with up to 4 mismatches on chr15 only (the STRC locus + paralog). For full off-target risk, repeat against full hg38 (~30x larger; not done in this run for time).
Gates
- Phase 4f passes if ≥1 of {salicylic, nicotinic, cyclopropane-phenyl-COOH} recovers ≥30% of the 8.4 kcal/mol E1659A interface penalty from STRC Electrostatic Analysis E1659A.
- PE off-target passes if the maternal-allele pegRNA has ≤5 off-target hits with ≤3 mismatches in chr15.
What Egor (parallel session) is doing
While these run, the other Claude session is doing:
- ASO Phase 1 ViennaRNA fold check on the 18nt candidates
- Strategy B mRNA-LNP cochlear tropism literature scan (20%/50% OHC gate)