Cortexa research tool·structure·visualization_protein_3d

Visualize Protein Structure 3d

Visualize 3D protein structures using py3Dmol. Supports PDB IDs, PDB file content, and various visualization styles including cartoon, surface, and stick representations. Prerequisites: Requires 'py3Dmol' package (install: pip install Cortexa Tool Mesh[visualization]).

Livelast probed 2026-04-30 23:07Z· 96msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 96ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "color_scheme": {
      "default": "spectrum",
      "description": "Color scheme for the structure",
      "enum": [
        "spectrum",
        "rainbow",
        "ssPyMOL",
        "ssJmol",
        "Jmol",
        "amino",
        "shapely",
        "nucleic",
        "chain",
        "default"
      ],
      "type": "string"
    },
    "height": {
      "default": 600,
      "description": "Height of the visualization in pixels",
      "type": "integer"
    },
    "pdb_content": {
      "description": "Raw PDB file content as string. Either pdb_id or pdb_content must be provided.",
      "type": "string"
    },
    "pdb_id": {
      "description": "PDB identifier (e.g., '1CRN', '7CGO'). Either pdb_id or pdb_content must be provided.",
      "type": "string"
    },
    "show_sidechains": {
      "default": false,
      "description": "Whether to show sidechain atoms",
      "type": "boolean"
    },
    "show_surface": {
      "default": false,
      "description": "Whether to show molecular surface",
      "type": "boolean"
    },
    "style": {
      "default": "cartoon",
      "description": "Visualization style",
      "enum": [
        "cartoon",
        "stick",
        "sphere",
        "line"
      ],
      "type": "string"
    },
    "width": {
      "default": 800,
      "description": "Width of the visualization in pixels",
      "type": "integer"
    }
  },
  "required": [
    "pdb_id",
    "pdb_content"
  ],
  "type": "object"
}

Examples (1)

Default Visualize Protein Structure 3d call

public-safeinput

{
  "height": 1,
  "pdb_content": "",
  "pdb_id": "1AKI",
  "show_sidechains": false,
  "show_surface": false,
  "width": 1
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_visualize_protein_structure_3d
Tool name: visualize_protein_structure_3d
Added: 2026-04-30 22:47Z
Tags: tooluniverse

Visualize Protein Structure 3d

Livelast probed 2026-04-30 23:07Z· 96msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "color_scheme": { "default": "spectrum", "description": "Color scheme for the structure", "enum": [ "spectrum", "rainbow", "ssPyMOL", "ssJmol", "Jmol", "amino", "shapely", "nucleic", "chain", "default" ], "type": "string" }, "height": { "default": 600, "description": "Height of the visualization in pixels", "type": "integer" }, "pdb_content": { "description": "Raw PDB file content as string. Either pdb_id or pdb_content must be provided.", "type": "string" }, "pdb_id": { "description": "PDB identifier (e.g., '1CRN', '7CGO'). Either pdb_id or pdb_content must be provided.", "type": "string" }, "show_sidechains": { "default": false, "description": "Whether to show sidechain atoms", "type": "boolean" }, "show_surface": { "default": false, "description": "Whether to show molecular surface", "type": "boolean" }, "style": { "default": "cartoon", "description": "Visualization style", "enum": [ "cartoon", "stick", "sphere", "line" ], "type": "string" }, "width": { "default": 800, "description": "Width of the visualization in pixels", "type": "integer" } }, "required": [ "pdb_id", "pdb_content" ], "type": "object" }