Protein Structure 3D Tools

Configuration File: protein_structure_3d_tools.json Tool Type: Local Tools Count: 1

This page contains all tools defined in the protein_structure_3d_tools.json configuration file.

Available Tools

visualize_protein_structure_3d (Type: ProteinStructure3DTool)

Visualize 3D protein structures using py3Dmol. Supports PDB IDs, PDB file content, and various vi…

visualize_protein_structure_3d tool specification

Tool Information:

  • Name: visualize_protein_structure_3d

  • Type: ProteinStructure3DTool

  • Description: Visualize 3D protein structures using py3Dmol. Supports PDB IDs, PDB file content, and various visualization styles including cartoon, surface, and stick representations.

Parameters:

  • pdb_id (string) (required) PDB identifier (e.g., ‘1CRN’, ‘7CGO’). Either pdb_id or pdb_content must be provided.

  • pdb_content (string) (required) Raw PDB file content as string. Either pdb_id or pdb_content must be provided.

  • style (string) (optional) Visualization style

  • color_scheme (string) (optional) Color scheme for the structure

  • width (integer) (optional) Width of the visualization in pixels

  • height (integer) (optional) Height of the visualization in pixels

  • show_sidechains (boolean) (optional) Whether to show sidechain atoms

  • show_surface (boolean) (optional) Whether to show molecular surface

Example Usage:

query = {
    "name": "visualize_protein_structure_3d",
    "arguments": {
        "pdb_id": "example_value",
        "pdb_content": "example_value"
    }
}
result = tu.run(query)