Optional Parameters

Input Options

-ligand_names <names>

If multiple ligands are in the structure but only a specific ones are desired, they can be specified here. Examples are either the three letter code “LIG”, or in case of a peptide “VAL-GLU-TYS-PHE-ALA”. Multiple different ligands, should be separated by commas, “LIG,GIL,INH”.

-map <filename>

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

-metadata <filename>

Metadata json file containing OEStructureMetadata. Using this can be a way to indicate desired ligands, tautomers to use for ligands, structure sequence etc, as well as structure title for output file names.

-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 indicate residue 25 in chain A, irrespective 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 spruce_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 spruce_settings.param, if no prefix is specified.

-verbose : Triggers copious logging output
-write_biounits

Option to write intermediate Bio-DesignUnits, which can be used with enumsites to site to potential allosteric sites later.

[default = false]

Split Parameters

-altloc <method>

Parameter determining how alternate locations are handled. The primary option, collapses alternate locations, whereas the enumerate option attempts to set detected alternate locations, A, B, etc.

[default = enumerate]

-cofactor_codes <codes>

Mechanism to define 3 letter codes that should be recognized as co-factors if not done automatically, e.g. “ATP”, or “ATP,NAD”

-excipient_codes

Mechanism to define 3 letter codes that should be recognized as excipients if not done automatically, e.g. “GOL”, or “GOL,DMS”

-make_packing_residues

Option to generate packing residues, both for visualization, but also for Iridium classification

[default = true]

-min_lig_atoms

Parameter determining the min number of atoms a ligand molecule can have. A reason to lower this number would be for small fragments that need to be classified as ligands

[default = 8]

-max_lig_atoms

Parameter determining the max number of atoms a ligand molecule can have. A reasons to increase this number could be for peptidic ligands

[default = 100]

-max_lig_residues

Parameter determining the max number of residues a ligand molecule can have. A reasons to increase this number could be for peptidic ligands

[default = 5]

-max_sys_atoms

Parameter limiting the max number of atoms in the entire system that spruce will allow for processing. If this limit is reached e.g. due to a large systems or symmetry expansion resulting in a larger than expected system, spruce will stop processing and return false.

[default = 50,000]

-target

Parameter telling the system what the “target” is. This is particularly helpful for systems containing both protein and nucleic acids, where the automated system does not correctly identify the nucleic acid as the target of interest. Allowed values are protein or nucleic.

[default = protein]

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)

Build Parameters

-build_cterm_caps

Option to cap broken c-termini in protein chains

[default = true]

-build_nterm_caps

Option to cap broken n-termini in protein chains

[default = true]

-build_sidechains

Option to build missing or partial protein sidechains

[default = true]

-delete_clashing_solvent

Option to allow build steps to remove clashing solvent

[default = true]

-rot_coverage <value>

Coverage of rotamer libraries to use, a lower number can be used to speed up side chain re-building skipping lower probability side-chain rotamers.

[default = 100.0]

-rot_library <value>

Rotamer library used for building sidechains and loops. Allowed values are ‘richardson2016’, ‘dunbrack’, ‘richardson’.

[default = richardson2016]

Prep Parameters

-charge_radii

Option to assign partial charge and radii

[default = true]

-protonate

Option add and optimize protons in the system

[default = true]

Protonation Parameters

-generate_tautomers

Option to generate and use tautomers in the hydrogen network optimization

[default = true]

-het_group_nbr_dist <value>

Distance between heterogens used to determine optimization clusters for protonation

[default = 3.5 (angstroms)]

-opt_expt_protons

Option to optimize hydrogens assigned in the experiment.

[default = false]

Biological Unit Extraction Parameters

-bu_superpose

Option to superpose the biological units

[default = false]

-max_bu_atoms

Option to limit the size of BUs processed based on number of atoms

[default = 50,000]

-max_bu_parts

Option to limit the size of BUs processed based on number of parts

[default = 24]

-min_align_score

Option to specify minimum sequence alignment score

[default = 200]

-pref_author_record

Option where the author BIOMT record is preferred over the software generated one

[default = true]