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PDB Writer

LigandScout Extensions for the KNIME Workbench version 1.7.9 by InteLigand GmbH

The PDB Writer node saves macromolecule complexes to PDB files.

Options

Settings

Output directory
Path to the output directory that should hold the created PDB files.
Output file name: Source file name
The output file name will be defined as the former file name of the macromolecule. An optional suffix can be added to differentiate it from the old file name.
(Default: The former file name of the macromolecule, no prefix)
Output file name: Macromolecule name
The output file name will be defined as the name of the macromolecule. An optional suffix can be added.
(Default: The name of the macromolecule, no suffix)
Output file name: Custom name
Use a custom file name to be used for each output file. The row number is added as a prefix to differentiate the files from each other.
Export Ligand
Export ligand molecules.
(Default: enabled)
Export Environment
Export the environment of the ligand.
(Default: enabled)
Include Hydrogens
If selected, hydrogens will be included in the output file. Unchecking this option can significantly decrease the output file size.
(Default: enabled)
gz Compressed
Compresses output in gz format.
(Default: disabled)
zip Compressed
Compresses output in zip format.
(Default: disabled)

Input Ports

Icon
Table containing the macromolecule(s) to write to the specified output PDB-file

Best Friends (Incoming)

Installation

To use this node in KNIME, install LigandScout Extensions for the KNIME Workbench from the following update site:

KNIME 4.3

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Developers

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