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PDB Visualization

Generates an HTML string for interactive protein structure visualization from a PDB input. Designed for previewing single PDB records; if a batch is provided, only the first (alphabetically) is visualized.

PDB Visualization

Quick Start

  1. Connect a node outputting a PDB to the PDB Visualization node.
  2. Run the workflow.
  3. Use the Output node to preview the protein structure interactively.

Setup Guide

1. Add the Node

  1. Insert the PDB Visualization node into your workflow.
  2. Connect a PDB output from any compatible node.

2. Preview the Structure

  1. Connect the output of this node to an Output node.
  2. Run the workflow to view the protein in an embedded viewer.

Basic Usage

Visualizing a Protein Structure

  • Use for quick inspection of a single PDB structure.
  • If a batch is provided, only the first record is shown.
  • Suitable for integration in protein design and analysis pipelines.

Configuration

Required Inputs

Field Description Type Example
pdb PDB to visualize. If a batch, only the first is shown. PDB { "1abc": "...PDB content..." }

Optional Inputs

None

Outputs

Field Description Example
html HTML string for protein preview. <!DOCTYPE html>...

Best Practices

Visualization

  • Use for single-structure visualization; batch support is not available.
  • Connect directly to an Output node for immediate preview.

Data Integrity

  • Ensure the PDB input is valid and contains at least one record.
  • For batch PDBs, verify the desired structure is first alphabetically if previewing a specific one.

Troubleshooting

Common Issues

  • No structure displayed: Ensure the input PDB is valid and not empty.
  • Batch input not fully visualized: Only the first PDB in a batch is shown; split batches if needed.

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