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Get PDB

Retrieves PDB structure(s) for the specified PDB code(s).

Backend implementation

$SCHRODINGER/utilities/getpdb
The command line tool getpdb is used to implement this node.

Options

PDB IDs: Specify comma separated list of PDB IDs and optional Chain IDs. Ex: PDB_ID[:Chain_ID],PDB_ID[:Chain_ID],... If an PDB_ID could not be downloaded in pdb format, the node will try to download in cif format and then convert to pdb format. In this case, the any chains specified are ignored as chains cannot be specified in cif format.
Include Biological unit: Download the complete biological unit for each PDB code. This option forces downloading from the RCSB respository. If switched ON, chains cannot be specified in the PDB names.
Fetching from: Choose the location to fetch the PDBs. If 'Local Installation Only' is selected, 'Include Biological unit' will be switched OFF and disabled.

Input Ports

This node has no input ports

Output Ports

: Molecules in PDB format

Views

This node has no views

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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