Optional Parameters

Input Options

-fit_lig <filename>

A file containing a ligand to use as a constraint during the superposition. Should only be used if the input is not an OEDesignUnit

-ref_lig <filename>

A file containing a reference ligand to use as a constraint during the superposition. Should only be used if the input is not an OEDesignUnit

Output Options

-prefix <prefix>

Prefix used to name output files, default is blank. To avoid overwriting input files, all structure files are automatically using the prefix superposed_ if no prefix is specified.

[default = superposition]

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix.

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix.

-verbose : Triggers copious logging output

Parameters

-method <method>

The method to use for superposition

Method	Description
global	Global Sequence Alignment to identify CA pairs
site	Global Sequence Alignment to identity CA pairs - focusing on the subset in active site
ddm	Superposition using the Distance Difference Matrix method (DDM)
sse	Superposition using an overlap of Secondary Structure Elements (SSE)
weighted	Superposition using Weighted DDM method
sitehopper	Superposition using SiteHopper