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PDB Visualization

Generates an embeddable HTML viewer for a protein structure. It uploads the provided PDB content to secure storage and returns a full-page HTML string that loads the structure in a Mol* (molstar.org) viewer. If a batch of PDBs is provided, only the first is visualized.
Preview

Usage

Use this node to preview a protein structure during or after a workflow that produces or loads PDB data. Connect a PDB dictionary output (e.g., from a loader, combiner, or predictor) to quickly render an interactive 3D view in the app. The node returns an HTML string that can be routed to an Output/Display node.

Inputs

FieldRequiredTypeDescriptionExample
pdbTruePDBProtein structure to visualize. Accepts a dictionary mapping an ID to PDB content. If multiple entries are provided (batch), only the first one is used.{"proteinA": "ATOM 1 N MET A 1 11.104 13.207 -2.222 1.00 20.00 N \n...\nEND"}

Outputs

FieldTypeDescriptionExample
htmlSTRINGHTML string that embeds a full-page Mol* viewer iframe loading the uploaded structure.Full Screen Protein Viewer......

Important Notes

  • Only the first structure in a batch is visualized.
  • The node uploads the structure to secure storage and uses a signed URL in an external Mol* viewer (molstar.org).
  • If extraction of a PDB from the input fails, the node returns the string "None".
  • Viewer controls are minimized (controls hidden, left panel collapsed) for clean embedding.
  • Execution priority is elevated so the preview is generated promptly when connected as an output node.
  • The input PDB should be valid text content; malformed or empty structures will fail to visualize.

Troubleshooting

  • If output is "None": Ensure the pdb input is a non-empty dictionary {id: pdb_content} with valid PDB text.
  • If the viewer shows a blank page: Verify the structure content is valid PDB and the signed URL remains accessible.
  • If uploads time out or fail: Check network connectivity and that backend services for uploading are available; try again later.
  • If you connected a batch and see a different structure than expected: Remember only the first available entry is used for visualization.
  • Large PDB files may take longer to upload and render; allow additional time or reduce structure size if possible.

Example Pipelines

Example
Example