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name: relaxation description: "Guide AlphaFold Amber/OpenMM relaxation, AmberRelaxation APIs, CPU/GPU relax choices, structural violation metrics, and PDB cleanup constraints." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

AlphaFold Relaxation

Use this sub-skill when a task is about AlphaFold's Amber/OpenMM relaxation step, AmberRelaxation, amber_minimize.run_pipeline, CPU versus GPU relaxation, PDBFixer/OpenMM cleanup failures, or structural violation metrics reported by relaxation.

Start Here

• Read references/workflows.md to decide whether to relax, how CLI relaxation maps to API calls, and when to switch GPU relaxation to CPU.
• Read references/api-reference.md for AmberRelaxation, amber_minimize, cleanup helpers, debug data, and violation metric contracts.
• Read references/troubleshooting.md for OpenMM platform errors, missing PDBFixer, poor residue definitions, atom-mask mismatches, repeated minimization failures, unstable GPU relaxation, and models_to_relax=none tradeoffs.
• Run scripts/check_relaxation_inputs.py on a candidate PDB to inspect ATOM records, residue coverage, single-residue chains, common backbone gaps, heterogens, and optional OpenMM/PDBFixer import availability without running minimization.

Routing Boundaries

• Use this sub-skill for alphafold.relax.relax.AmberRelaxation, alphafold.relax.amber_minimize, alphafold.relax.cleanup, alphafold.relax.utils, OpenMM/PDBFixer relaxation backend behavior, and structural violation metrics.
• Use ../prediction-cli/ for choosing top-level --models_to_relax, constructing run_alphafold commands, MSA reuse, model/database presets, and output-directory orchestration.
• Use ../outputs-and-confidence/ for interpreting relaxed_*.pdb, unrelaxed_*.pdb, ranked_*.pdb, relax_metrics.json, pLDDT, PAE, pTM, ipTM, AFDB, or AlphaFold Server outputs after files exist.
• Use ../model-config-and-api/ and the root troubleshooting guidance for shared package/backend conflicts involving JAX, OpenMM, CUDA, TensorFlow, NumPy, or installed dependency pins.

Safe Operating Rules

• Do not run Amber relaxation, OpenMM minimization, or full AlphaFold prediction during routine validation; relaxation can require working OpenMM platforms and can be slow or hardware-sensitive.
• Treat --models_to_relax=none as a valid troubleshooting or exploratory choice when OpenMM/PDBFixer is failing; explain that structures may retain distracting stereochemical violations.
• Prefer CPU relaxation for stability triage when CUDA/OpenMM errors, GPU nondeterminism, or GPU platform availability is the suspected blocker; warn that CPU relaxation is usually slower.
• Treat relaxation as a stereochemical cleanup step, not a confidence-improvement step. It should not change pLDDT/PAE interpretation, and output confidence routing belongs in ../outputs-and-confidence/.
• Keep public guidance environment-neutral: use package APIs and user-owned paths, not local inspection environment paths or source-checkout-only fixtures.

Bundled Helper

python sub-skills/relaxation/scripts/check_relaxation_inputs.py ranked_0.pdb --check-imports --json

The helper is standalone, uses only the Python standard library by default, and never imports AlphaFold, runs PDBFixer cleanup, creates an OpenMM system, or performs minimization.