internscience 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"msgimage_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.