Optional Parameters

Input Options

-map <filename>

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

Accepted formats are structure factor CIF files (.cif, .cif.gz) and legacy MTZ files (.mtz). See OEReadMTZ in the OEChem TK manual for MTZ map and column conventions.

-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”, e.g. “ASP:25: :A” indicating Aspartic acid 25 in chain A. Note: A blank/whitespace character is used for the insert code, which is a typical use case.

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_file <settingsfile>

(Alias: -settings)

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]

See also

-add_style

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

[Default=true]

See also

-collapse_nonsite_alts

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

[Default=true]

See also

-duplicate_removal

Option to deduplicate identical structures resulting from symmetry operations

[Default=true]

See also

-enum_cofactors_sites

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

[Default=false]

See also

-restrict_to_refsite

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

[Default=true]

See also

-site_size <value>

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

[Default=5.0 (angstroms)]

See also

-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]

See also

-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)

weighted

Superposition weighting residues by B-factor or occupancy

sitehopper

Superposition based on binding site similarities (sitehopper)

GlobalSequence

Alias for global — Global Sequence Alignment to identify CA pairs

DDMatrix

Alias for ddm — Superposition using the Distance Difference Matrix method

SiteSequence

Alias for site — Global Sequence Alignment focusing on the active site

See also