molclaw-visualize-protein

name	molclaw-visualize-protein
description	Render a server-side PDB protein structure as a PNG with the MolClaw MCP tool `visualize_protein`.
license	MIT license
metadata	{"skill-author":"PJLab","skill-level":"L1-Tool","version":1}

MolClaw Protein Visualization

Use the live MCP tool visualize_protein when the task needs an image of a protein structure from a PDB file.

This tool renders the structure only. It does not repair a PDB or calculate protein–ligand interactions. Use fix_pdb before visualization when structural cleanup is required, and use interaction_visualizer for residue-level interaction analysis.

Input

The live schema has one required field:

Field	Type	Meaning
pdb_file_path	string	Server-side path to a PDB file

Use the path returned by protein retrieval, prediction, or fix_pdb. For a local PDB, upload it with the MolClaw file-transfer tool first. Do not pass a local workspace path or fabricate a server path.

MCP call

<tool_call>{"tool_name":"visualize_protein","arguments":{"pdb_file_path":"<artifact:structure/protein.pdb>"}}</tool_call>

Output

On success, the result contains:

• status: "success"
• msg
• image_path: server-generated PNG path

Treat the returned PNG as the authoritative visualization artifact. In Drug-Pipe online inference, its raw server path is converted to a canonical artifact reference before entering model-visible context or the final answer.

If the tool reports a missing or invalid PDB, preserve the error observation, obtain or repair a valid server-side PDB, and retry only when justified.