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Load PDB

Loads PDB content from a string and assigns a unique ID for use in downstream workflows. The output is a dictionary with the PDB ID as the key and the PDB string as the value.

Load PDB

Quick Start

  1. Enter or paste your PDB string.
  2. Specify a unique PDB ID (match with FASTA if needed).
  3. Connect the output to downstream nodes.

Setup Guide

1. Prepare PDB Input

  1. Obtain or generate your PDB string.
  2. Ensure you have a unique identifier for this PDB.

2. Node Configuration

  1. Input the PDB string in the provided field.
  2. Set the PDB ID (default is "pdb").
  3. Connect the output to other nodes as required.

Basic Usage

Single PDB Loading

  • Load a single PDB structure for use in a workflow.
  • Assign a unique ID to ensure compatibility with batch and sequence nodes.

Configuration

Required Inputs

Field Description Type Example
pdb_string PDB string to upload. STRING ATOM ...
pdb_id ID assigned to this PDB. Should be unique if using multiple PDBs. STRING 1abc

Optional Inputs

None

Outputs

Field Description Example
structure.pdb Dictionary with pdb_id as key and pdb_string as value. {"1abc": "ATOM ..."}

Best Practices

Unique Identification

  • Always assign a unique PDB ID, especially when using multiple PDBs in a workflow.
  • Match the PDB ID with the corresponding FASTA sequence ID if both are used.

Data Integrity

  • Validate your PDB string for formatting errors before uploading.
  • Use descriptive IDs to simplify workflow management.

Troubleshooting

Common Issues

  • Duplicate PDB IDs: Ensure each PDB has a unique ID to avoid downstream errors.
  • Invalid PDB Format: Check that the PDB string is correctly formatted and complete.

Need Help?

  • Contact support for further assistance.