The simplest way to run EnumSites is by passing in an unprepped, biounit OEDesignUnit file (oedu) as the input and a fully prepared OEDesignUnit file as a reference.
prompt> enumsites -ref 4OBD_AB__DU__E-2-PGNFFQNRP-10.oedu -in 1HHP_AB__DU__biounit.oedu
Here, EnumSites will use the biounit OEDesignUnit 1HHP_AB__DU__biounit.oedu with the -in parameter, along with a reference OEDesignUnit file 4OBD_AB__DU__E-2-PGNFFQNRP-10.oedu with the -ref option, in order to create OEDesignUnits from 1HHP_AB__DU__biounit.oedu using the sites defined in the reference structure. The output will be a set of OEDesignUnit (.oedu) files.
Instead of a fully prepared OEDesignUnit file as a reference, one may simply specify the site residues required to define the new site of interest.
So for example:
prompt> enumsites -site_residue "ASP:25: :A" -in 1HHP_AB__DU__biounit.oedu
will construct OEDesignUnits based on enumeration of sites from the same biounit OEDesignUnit file as before (1HHP_AB__DU__biounit.oedu), but here the definition of the site comes from the -site_residue option instead of another fully-prepared OEDesignUnit.
To calculate the Iridium classification as a metric of structure quality with enumsites, one must provide the map file that corresponds to experiment from which the biomolecular structure was derived:
prompt> enumsites -site_residue "MET:124: :A" -map 1a29.mtz -in 1A29_A__DU__biounit.oedu
Here a set of OEDesignUnit files will be produced from 1A29_A__DU__biounit.oedu and the site defined as MET:124: :A, but the Iridium classification can be made since the MTZ file (1a29.mtz) was passed in through the -map option.
To prevent continually over-writing output files, the -prefix flag allows you to give unique names to these files.
prompt> enumsites -site_residue "ASP:25: :A" -in 1HHP_AB__DU__biounit.oedu -prefix FOO_
will write the output structures into a file named FOO_1HHP_AB__DU__apo_ASP_A-25.oedu.