Optional Parameters

Input Options

-map <filename>

Input electron density map from X-ray crystallography, to be used for Iridium score calculation.

-ref <filename>

Reference OEDesignUnit indicating the proper biological unit and relevant binding site.

-site_residue <residue identifier>

Input option to specify a binding site using a single residue specification if apo (or holo). The format is “name:num:insert code:chainid:[fragment number:alternate location]”, e.g. “ASP:25: :A:.*: :”, indicating Aspartic acid 25 in chain A, also ensuring both the insert code and alternate location is not set, while the fragment number can be anything (the regex .* fuzzy matcher). The fragment number and alternate location can be left out, in which case they will automatically be replaced by fuzzy matchers. While you could specify ”.*:25: :A”, which would incidate residue 25 in chain A, irrespecive of the residue type, however, we recommend being as explicit as possible.

Output Options

-prefix <prefix>

Prefix used to name output files, default is blank

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix. The default will be enumsites_output.log, if no prefix is specified.

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix. The default will be enumsites_settings.param, if no prefix is specified.

-verbose : Triggers copious logging output

Enumerate Sites Parameters

-add_interactions

Option to add OEInteractionHints to the design unit(s)

[default = true]

-add_style

Option to add visualization style to the design unit(s)

[default = true]

-collapse_nonsite_alts

Option to deduplicate structures with different alternate locations if those alternate locations are far from the binding site

[default = true]

-duplicate_removal

Option to deduplicate identical structures resulting from symmetry operations

[default = true]

-enum_cofactors_sites

Option to generate design units with sites based on components classified as co-factors

[default = false]

-restrict_to_refsite

Option to skip generating design units for sites identified, that do not match a provided reference design unit

[default = true]

-site_size <value>

Distance from the ligand used to determine the size of the site

[default = 5.0 (angstroms)]

-superpose

Option to superpose generated design units, if multiple. If a reference is provided, the first generated design unit will be superposed onto the reference structure, and subsequent structures onto that one.

[default = true]

-superpose_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)