PDB Downloader (Source)

This node, and the corresponding manipulator node, allows the downloading of structure and sequence files from the RCSB PDB . The formats supported are:

PDB
mmCIF
Structure Factors
PDBML
FASTA Format Sequence
NMR Restraints
NMR Restraints v2
NMR Chemical Shifts

PDB files are cast as PDB cells, and PDBML as XML cells. No checking the the structure IDs is carried out - invalid IDs will return cells containing missing values. WARNING - the PDBML option can result in very large tables!

This node was developed by Vernalis (Cambridge, UK) . For feedback and more information, please contact knime@vernalis.com

Options

Enter a PDB ID: Enter a PDB ID, or list of PDB IDs separated by ';'
Downloaded Files: Select the desired file format(s) from the available options
Select All: Selects all options in the Downloaded Files option list
Clear: Clears the selection and returns it to the default (PDB only) selection

Input Ports

This node has no input ports

Output Ports

: Output table with the downloaded file(s)

Popular Predecessors

Popular Successors

Views

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Workflows

PDB REMARK 1KNIME Forum

Developers

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Installation

To use this node in KNIME, install the extension Vernalis KNIME Nodes 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: Vernalis Research, UK

Plugin version: 1.36.5.v202312061029

On NodePit since: 2023-12-06

Last update: 2024-04-18

Tags: Streamable

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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