PDB Visualization¶
Generates an HTML string that renders an interactive 3D protein structure viewer for a provided PDB. If a batch of PDBs is supplied, it automatically selects and visualizes the first one. The output is a full-page HTML viewer suitable for direct display in an app or browser.
Usage¶
Use this node at the end of a workflow when you want to preview a protein structure. Connect a PDB output (e.g., from Load PDB, PDB Combiner, or upstream processing nodes) to this node, then send the resulting HTML to your app's output or a display/output node to render the interactive viewer.
Inputs¶
| Field | Required | Type | Description | Example |
|---|---|---|---|---|
| pdb | True | PDB | PDB structure(s) to visualize. Accepts a dictionary mapping IDs to PDB content; if multiple are provided (batch), only the first entry is visualized. | {'protein_A': 'ATOM 1 N MET A 1 11.104 13.207 8.678 1.00 44.46 N \nATOM 2 CA MET A 1 12.560 13.445 8.459 1.00 43.27 C \nEND'} |
Outputs¶
| Field | Type | Description | Example |
|---|---|---|---|
| html | STRING | An HTML document as a string that embeds an interactive protein viewer for the provided PDB. |
Important Notes¶
- Only the first PDB in a batch is visualized. If you need to visualize a different entry, provide it as a single PDB or reorder your inputs.
- The viewer is loaded from an external visualization service. Network access is required for the embedded viewer to load correctly.
- If the PDB cannot be extracted or uploaded for preview, the output may be the string "None" instead of HTML.
- Best used as a terminal/preview step in a workflow to display the structure to end users.
Troubleshooting¶
- Viewer is blank or not loading: Ensure you have network access and that external viewer domains are not blocked by your environment.
- Output is "None": Verify the input PDB is valid and non-empty; for batches, confirm the first item contains a proper PDB string.
- Wrong structure visualized: If using a combined/batch PDB input, remember this node visualizes the first available entry. Provide the intended PDB as a single input or adjust the batch order.
- Security/content policies: If your environment restricts external iframes, allowlist the viewer domain or render the HTML in a permitted context.
Example Pipelines¶
