PDB Visualization¶
Generates a self-contained HTML page to visualize a protein structure from a provided PDB string. The node uploads the PDB content to a backend service to obtain a publicly accessible structure URL, then embeds it in a Mol* (molstar.org) iframe viewer with a full-screen layout.
Usage¶
Use this node when you have a protein structure in PDB format and want an immediate, shareable visualization. Typical workflow: load or generate a PDB string, pass it to this node, and use the returned HTML to display the interactive 3D viewer in a web panel or save it for external viewing.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb_string | True | STRING | The full PDB file contents as a string. This should be a valid PDB-formatted text representing the protein structure. | HEADER EXTRACELLULAR MATRIX 01-JAN-00 ATOM 1 N MET A 1 11.104 13.207 2.100 1.00 20.00 N |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| html | STRING | A complete HTML document string containing a full-screen Mol* iframe viewer for the uploaded protein structure. |
Important Notes¶
- The node relies on an external service to upload the PDB content and return a public structure URL; network connectivity and service availability are required.
- If the upload service returns a non-200 response or fails, the node raises an exception containing the status and error detail.
- The returned HTML is a full document with an embedded Mol* viewer configured to hide controls and collapse the left panel for a clean, full-screen view.
- Ensure the resulting structure URL is publicly accessible so the Mol* viewer can fetch and render the structure.
- Large PDB inputs may take longer to upload; the node uses an extended timeout for the upload request.
Troubleshooting¶
- Upload failed with error status: Verify the backend upload service is reachable, credentials/config (if any) are set up, and the PDB string is valid. Retry after checking network stability.
- Viewer displays blank or fails to load: Confirm the generated structure URL is publicly accessible and correctly encoded. Check browser console for blocked requests or CORS issues.
- Malformed PDB input: Validate the PDB format. Incorrect or corrupted content may cause the upload service to reject the input or Mol* to fail rendering.
- Slow loading times: Large structures or slow networks can delay loading. Consider simplifying the structure or ensuring faster network access.
Example Pipelines¶
