PDB Visualization¶
Generates a full HTML page that visualizes a protein structure (PDB format) using the Mol* web viewer. It uploads the provided PDB string to a backend service, obtains a temporary structure URL, and embeds it in an iframe for interactive viewing.
Usage¶
Use this node when you have a protein structure in PDB text format and want an immediately viewable, shareable HTML visualization. Typically used after a structure prediction or retrieval step to present results to end users or to embed the visualization in a report or UI.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb_string | True | STRING | The complete protein structure in PDB text format. This content is uploaded to a backend service to generate a viewable structure URL. | 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 standalone HTML document containing an iframe with the Mol* viewer preloaded to display the provided PDB structure. |
Important Notes¶
- This node depends on an external backend endpoint to upload the PDB text and return a structure URL; internet connectivity is required.
- If the upload request fails or the backend returns a non-200 response, the node raises an error with the reported status and message.
- The output is a full HTML page intended for embedding/display; ensure your consuming environment supports rendering iframes.
- The visualization uses the public Mol* viewer hosted at molstar.org; network or CSP restrictions may affect loading.
- Large PDB inputs can increase upload time and processing latency.
Troubleshooting¶
- Upload failed with non-200 response: Verify the backend service is reachable and credentials/configuration (ENDPOINTS) are correct; check the error message returned by the service.
- Viewer does not load or stays blank: Ensure internet access to molstar.org and that your environment allows iframes; check browser console for CSP or network errors.
- Invalid or malformed PDB: Validate the PDB string format; some services reject nonstandard or corrupted inputs.
- Slow or timed-out requests: Reduce PDB size if possible, retry on a more stable connection, or adjust timeout/settings if available in your environment.
Example Pipelines¶
