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Prime Build Homology Model

Schrödinger extension for KNIME Workbench version 21.1.156.202102141445 by Schrödinger

Build homology models using Prime starting from a pairwise sequence alignment.

Backend implementation

scripts/bldstructCLI.py run by cmdRunner.py
The script bldstructCLI.py is passed to cmdRunner.py to implement this node.

Options

Include Log in output
Include the Prime Homology Model log in the output data table
Maximum insertion size
Do not build insertion larger than the specified size
Ligands and cofactors to include
Specify a comma separated list of ligands and cofactors to include from this template. The format of the specification is AAA C:### where AAA is the ligand’s three letter code, C is its chain ID, ### is its residue number. Multiple ligands from the template are numbered using i as an index, starting from zero.
Tail building options
  • build to outermost aligned residue
  • omit tails entirely
  • build complete tails
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: PrimeBuild
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option from command line, just specify the option_name and the value as _off_ through the flow variable.

To pick the value from a column in the input table, specify the option_name and the value as :column_name: through the flow variable. Any column other than String, Integer and Double types will be written to a file and the file name is added as the option value.

Input Ports

Icon
Alignments in Maestro format

Output Ports

Icon
Homology model in Maestro format

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.3

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Developers

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