name: phenix-tools-reference description: Reference of available Phenix commands for structural biology analysis category: domain metadata: version: "1.0.0"

Phenix Tools Reference

If Phenix is available, prefer run_phenix_tool over execute_code for structural biology tasks like validation, superposition, refinement, and map analysis. Phenix is the gold standard for these tasks.

Call run_phenix_tool(tool_name="phenix.<command>", input_files=["file.pdb"], description="..."). This reference lists the most useful commands grouped by task. Most commands accept PDB or mmCIF files, but some take map files, reflection data, sequences, or other formats — check each tool's --help if you are unsure.

Validation and Quality Assessment

Example: Full validation

run_phenix_tool(
    tool_name="phenix.molprobity",
    input_files=["structure.pdb"],
    description="Comprehensive structure quality check",
)

Structure Comparison and Superposition

Example: Per-residue distances

run_phenix_tool(
    tool_name="phenix.model_model_distances",
    input_files=["experimental.pdb", "predicted.pdb"],
    description="Per-residue distances between experimental and predicted",
)

AlphaFold and Predicted Models

Example: Process AlphaFold model

run_phenix_tool(
    tool_name="phenix.process_predicted_model",
    input_files=["alphafold_model.pdb"],
    arguments={"pae_json_file_name": "alphafold_pae.json"},
    description="Process AlphaFold model and trim low-confidence regions",
)

Refinement

Refinement commands are compute-intensive and may approach the 5-minute timeout. Use targeted refinement when possible. The last four rows above are narrow-use — do not invoke unless the task explicitly calls for QM/magnetic/aspherical refinement.

Map Operations

Model Building and Manipulation

Example: Extract a single chain

run_phenix_tool(
    tool_name="phenix.pdbtools",
    input_files=["multimer.pdb"],
    arguments={"selection": '"chain A"', "output.file_name": "chain_A.pdb"},
    description="Extract chain A from multimer",
)

Ligand Tools

Data Analysis

Molecular Replacement

Sequence and Annotation

Useful Utilities

Tips for Using run_phenix_tool

1. Start with phenix.molprobity for a quick quality overview.
2. Input files are relative to data/.
3. Pass CLI arguments as arguments={"flag": "value"}.
4. Avoid large refinement jobs that are likely to hit the 5-minute timeout.
5. Check phenix.pdbtools before writing custom PDB manipulation code.
6. Use phenix.pdb_as_cif or phenix.cif_as_pdb for format conversion.