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Run PyMOL

Schrödinger extension for KNIME Workbench version 19.3.13.201908262231 by Schrödinger

Launch PyMOL

Backend implementation

PyMOL executable
The pymol.exe is used to implement this node.
Notes:
If "PyMOL executable" in Schrodinger preference page is set to some path, then for any new node, the default value of "PyMOL executbale" in the configuration panel will be filled with the path set in the preference.
If PYMOL4MAESTRO environment variable is set, then this will be given more precedence and considered as the PyMOL executable. If such an environment variable does not exist, then the value from the configuration panel will be used.
If none of these is set, then the node will try to get the PyMOL executable path automatically by checking the standard locations.

This node will not be executed in a batch mode.

Options

Column containing input
Column in the input data table containing molecules in Maestro, SD, Pdb or Mol2 format
PyMOL location
Choose a directory location containing PyMOL executable or directly choose a PyMOL executable/startup file. If empty, the location will be taken from the PYMOL4MAESTRO environment variable.
Pre-processing Command Script
These set of commands are executed just before the set of commands in Command Script area. If disabled, default set of commands, mainly to load the input file, will be executed. If enabled, user can edit this section to execute the preferred commands.
Note: %input_1% will be replaced by the actual input filepath.
Command script
A PyMOL command script entered into this field will be executed after PyMOL has been started.

To specify the basename of input files, use '%PyMOL_basename%'.
Ex: If the Command script has %PyMOL_basename%, then it will be replaced by basename of the input files.

To specify the flow variables, use %flowvar_name% in the command line.
Ex: If "Command script" has "%myvar1%" and if there exists a flow variable "myvar1" or "PyMOL|myvar1", then its value will get substituted in the command script.

Note: This node adds a flow variable PyMOL_basename to its 'Variable Outport', so that the basename of the files created by this node can be accessed by the downstream nodes

Input Ports

Molecules in Maestro, SD, Pdb, or Mol2 format

Best Friends (Incoming)

Workflows

Installation

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

KNIME 4.0
Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.

Developers

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