run_rosetta_scripts
Execute a RosettaScripts XML protocol on a given PDB file. Use this to run custom Rosetta protocols requiring the rosetta_scripts binary.
Instructions
Run a RosettaScripts XML protocol on an input PDB file. Use when executing Rosetta protocols. Requires local installation with rosetta_scripts binary.
Tool call template
Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"arguments": {
"xml_path": "<xml_path>",
"input_pdb": "<input_pdb>",
"out_dir": "<out_dir>"
},
"name": "run_rosetta_scripts"
}
}Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| exe_path | No | Path to rosetta_scripts executable (optional if on PATH) | |
| xml_path | Yes | Path to Rosetta XML protocol | |
| input_pdb | Yes | Path to input PDB | |
| out_dir | Yes | Output directory | |
| extra_flags | No | Additional command-line flags |