Surface Writer

This node writes the Positive, Negative, Van der Waals and Hydrophobic surfaces for the input molecules to a directory. The surfaces can be written in ccp4, cube, insight or moe format.

This node wraps the Forge™ executable 'fsurface', which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the 'Cresset Home' preference setting or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the 'fsurface Path' preference setting or the CRESSET_FORGESURFACE_EXE environment variable to point directly at the executable itself.

For more information visit www.cresset-group.com or contact us at support@cresset-group.com.

Options

Ports

Column containing the molecules
The column in the input datatable containing the molecules.

Input

Assign formal charges to input molecules
If checked, the protonation states for the input molecules will be set using Cresset's charging rules. Acids will be deprotonated, primary amines protonated, etc.

Surfaces to export

Positive
If checked, the positive field surfaces will be exported.
Negative
If checked, the negative field surfaces will be exported.
Van der Waals
If checked, the Van der Waals field surfaces will be exported.
Hydrophobic
If checked, the hydrophobic field surfaces will be exported.

Output

Format
The file format to save the surfaces as.
Quality
The quality of the surfaces.
Overwrite Directory
If checked the output directory will be overwritten.
Selected Directory
The directory where the surfaces will be written to.

Input Ports

Icon
The molecules to write the surfaces for.

Output Ports

This node has no output ports

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Links

Developers

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Installation

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

v5.3

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

Plugin provider: www.cresset-group.com
Plugin version: 2.8.0.230502
On NodePit since: 2024-09-27
Last update: 2024-11-23
KNIME versions: Since v3.6

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