Prime Build Homology Model

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.

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Workflows

• Model building 1KNIME Hub
• Model building 1-2KNIME Hub
• Model building 1-3KNIME Hub
• Model building on a template 1KNIME Hub
• Model building on a template 1-2KNIME Hub
• Protein model buildingKNIME Hub

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