This node is currently not available in KNIME v5.4 — instead we’re showing this page for KNIME v5.2. You can use the version menu in the title bar to permanently switch your preferred version. This will also show the link to the update site.

PDB Reader

Read molecules in PDB format.

To remove files from the list select the file and press the 'Delete' key.

To select all files in the list press Ctrl-A.

To add all files that match a pattern, using an asterisk (*) into the dialog "File Name" field. Press return, and the file filter will show up in the "Files of Type" drop down, then press Ctrl-A to select all of the files that show up with that filter. The list of files will then show up in the "File Name:" field, space delimited with double quotes around each file name. Then press "Open" to load all of those files.

Options

File Name: The name of the file to be loaded
File can be an URL like:
knime://LOCAL/path/to/file - knime://LOCAL refers to the current workspace
knime://knime.workflow/path/to/file - knime://knime.workspace refers to the current workflow
Import all structures: Whether the entire file should be loaded
Start: If not all structures are loaded, which number structure should loader start at (disabled if Import all structures is set)
End: Should the file be loaded until to end (disabled if Import all structures is set)
Total: If not all structures are imported and not loaded until the end, how many total structures should be loaded (disabled if Import all structures or End is set)

Input Ports

This node has no input ports

Output Ports

: Molecules in PDB format

Popular Predecessors

Popular Successors

Views

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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: 2024-12-18

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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