| name | structural_build |
| description | Orchestrator for macromolecular structure building pipelines. Routes tasks to sub-skills (chimerax, isolde, phenix, ccp4, emerald) and tools (Merizo). Use when the user asks to build/refine a structure, fit a model into a map, or run a multi-step structural biology workflow. NOT for single-tool tasks — use chimerax/isolde/phenix/ccp4/emerald directly. |
Structural Build — Orchestrator
Routes multi-step structure determination workflows to the right sub-skill.
Sub-skills
| Skill | Mode | Use for |
|---|
| chimerax | --nogui batch | Rigid-body fitting, editing, measurements, format conversion |
| isolde | GUI + REST | Flexible fitting (MDFF), local geometry fixes, ligand sim |
| phenix | CLI | Final refinement, validation, ligand restraints |
| ccp4 | CLI | Refmac5, Servalcat, AceDRG, MTZ preflight, explicit CCP4 binaries |
| emerald | CLI | Rosetta EMERALD ligand docking into cryo-EM density |
External Tools
| Tool | Location | Notes |
|---|
| Merizo | <MERIZO_INSTALL>/ | Domain segmentation (any structure, no PAE needed) |
| AlphaFold DB | via ChimeraX alphafold match | Template retrieval |
Task → Skill Routing
| Task | Skill |
|---|
| Delete/mutate/renumber/combine | chimerax |
| Rigid-body fitting (fitmap), superposition | chimerax |
| Domain-wise rigid-body fitting | chimerax (standalone Python script) |
| Flexible fitting into map (MDFF) | isolde |
| Fix Ramachandran/rotamer outliers, pepflips | isolde |
| MDFF with ligands | isolde (see ligand pre-flight checklist) |
| Domain decomposition | Merizo |
| Final refinement (real-space, Phenix route) | phenix |
| Reciprocal-space refinement with Refmac5 | ccp4 |
| Cryo-EM final refinement with Servalcat | ccp4 |
| Cryo-EM ligand docking with Rosetta EMERALD | emerald |
| Ligand restraint generation (eLBOW) | phenix |
| Ligand restraint generation (AceDRG) | ccp4 |
| Metal coordination restraints | phenix (.edits file) |
| SS restraints | phenix (with helix_type fix) |
| Q/N/H flip correction | phenix (reduce) |
| Validation (MolProbity) | phenix |
Cryo-EM Pipeline (AlphaFold → Map)
1. Global rigid-body fitting (ChimeraX --nogui)
Center model on map → fitmap search 500 → local refine
Quality gate: ≥60% atoms in density
2. Domain segmentation (Merizo)
--iterate → domain boundaries + NDR regions
3. Conservative trim (ChimeraX --nogui)
Remove residues: unassigned by Merizo AND no density (0.5σ)
4. Domain-wise rigid-body fitting (ChimeraX --nogui, Python script)
Per-domain fitmap, capture model.position delta (NOT atom.coord!)
Linker interpolation (SLERP + LERP), DNA local-only
Never extract+reassemble — fit copies, apply transforms to complete model
5. ISOLDE flexible fitting (10 min) (ChimeraX GUI + REST)
Pre-flight: OP3/OXT delete, addh, map association, MDFF verify
Internal Python timer (REST hangs during sim)
Monitor ih.simulation_running every 30s
6. Post-ISOLDE cleanup block
6a. Aggressive trim (chain ends + internal gaps ≥5)
6b. Check for breaks → fill gaps from pre-trim model
6c. ISOLDE touch-up (2-5 min) to relax filled regions
7. Ligand building (if applicable)
7a. Place ligands from reference structures (superpose + extract)
7b. ISOLDE with ligands (5 min) — full pre-flight checklist
Fix ADP H-naming, delete OXT, check post-PRO HIS, set OpenCL
7c. For cryo-EM small-molecule docking into density, run Rosetta EMERALD
when no trustworthy transferred pose exists or multiple orientations remain plausible
7d. Prepare restraint files: metal .edits, ligand .cif, SS .eff
8. Phenix real-space refinement (Phenix CLI)
Iterative: R1 conservative → check → tighten → R2
Fix helix_type *unknown → *alpha
Apply Q/N/H flips (reduce) between rounds
Don't use crystal reference_model at >3Å
9. Validation (Phenix MolProbity)
Targets: Rama <0.5%, favored >96%, rotamer <2%, clashscore <10
10. Rotamer outlier fix (if rotamer >2%) (ChimeraX + ISOLDE + Phenix)
Three-phase protocol — see "Rotamer Fix Protocol" section below.
11. Iterate or deposit
Max 3 ISOLDE↔Phenix cycles before flagging
## Rotamer Fix Protocol
When rotamer outliers exceed ~2% after Phenix refinement, use this three-phase approach:
### Phase 1: Triage + Fix (ChimeraX --nogui or GUI, swapaa)
1. Run `phenix.rotalyze model.pdb` → list all OUTLIER residues
2. For each outlier, sample map density at side-chain atoms (skip N/CA/C/O):
- `avg > 0.15` → **GOOD_DENSITY** (real conformation in density)
- `0.05 < avg < 0.15` → **WEAK_DENSITY**
- `avg < 0.05` → **NO_DENSITY**
3. Fix each outlier in ChimeraX with `swapaa`:
- **GOOD_DENSITY:** `swapaa /<chain>:<res> <resname> criteria d` (density-fit best rotamer)
- **WEAK_DENSITY:** `swapaa /<chain>:<res> <resname> criteria c` (chi-angle nearest allowed)
- **NO_DENSITY:** `swapaa /<chain>:<res> <resname> criteria c` (common rotamer)
4. Save intermediate model
### Phase 2: Targeted ISOLDE (5 min, selection only)
1. Load rotamer-fixed model + map in ChimeraX GUI
2. Run full ISOLDE pre-flight (OP3, OXT, addh, map association, MDFF verify)
3. **Find Volume by type, not index** (see isolde skill rule 2b)
4. Select all outlier residues: `select #1 & (/<chain>:<res> ...)`
5. Expand selection: `select zone sel 5.5 #1 & protein`
6. Start sim on selection: `isolde sim start sel`
7. 5 min timer → stop + save (strip H first)
### Phase 3: Gentle Phenix cleanup
1. Run `phenix.real_space_refine` with:
- `macro_cycles=3`
- `run=minimization_global` only (NO `local_grid_search` — preserves ISOLDE improvements)
- Keep SS, metal, ligand restraints active
2. This fixes Rama/Cβ regressions from ISOLDE dynamics without disturbing rotamers
### Expected results (at 3.3 Å)
- Rotamer outliers: 2.5% → ~1.0%
- Clashscore: improved
- Rama favored: maintained or improved
- MolProbity: significant improvement
X-ray Pipeline
ChimeraX: open model + MTZ
→ ISOLDE: interactive refinement with live maps
→ Export to chosen refinement engine
→ Phenix: phenix.refine + validation
OR
→ CCP4: MTZ preflight → Refmac5 + validation
Quick Model Editing (no simulation)
ChimeraX only: delete, mutate, renumber, combine, addh, dockprep
Data Flow
Input:
model.cif — AlphaFold/predicted model
map.mrc — CryoSPARC/RELION map
Intermediate (sequential numbering, NEVER overwrite):
model_2_fitted.cif → model_3_trimmed.cif
→ model_4_domainfit.cif → model_5_isolde.cif
→ model_6_trimmed.cif → model_7_gapfilled.cif
→ model_8_isolde.cif → model_9_ligands.cif
→ model_10_isolde.cif → model_N_phenix.pdb
Restraint files:
ss.eff — SS restraints (helix_type fixed)
metal_restraints.edits — metal coordination
ligand.cif — from eLBOW
Key rule: Always save to NEW filename. ChimeraX caches files.
Integration Notes
- ChimeraX ↔ ISOLDE share session via REST — model IDs consistent
- ISOLDE → Phenix: export
.eff with self-reference torsions, disabled rotamer/rama/SS
- Refmac5, Servalcat, AceDRG, and MTZ preflight/inspection run through the
ccp4 skill
- Rosetta EMERALD density-guided ligand docking runs through the
emerald skill
- Merizo runs in separate Python venv — output parsed by agent
- ISOLDE uses OpenMM templates (NOT Phenix .edits) — different restraint systems
- Metal restraints: ISOLDE handles via
metal_name_map, Phenix via .edits file
