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”.

See also

-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). Structure factor CIF files are the current format provided by the RCSB; MTZ files are supported for backward compatibility.

-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. The -generate_tautomers option should be set to false and -opt_expt_protons to true to only consider the desired ligands. More details along with an example metadata file can be found at Creating OEDesignUnits Using Provided Metadata. The OESpruce::OEStructureMetadataToJson fucntion can be used to create an appropriate json file as well.

See also

-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.

See also

-add_receptors

Option to add OEReceptors onto the design units

[Default=true]

See also

Output Options

-out <out>

Write to a user specified file. Enforces *.oedu format. Can be used with -warts to write multiple files, one per design unit.

-warts

Option to add warts “_#” to the user supplied filename, when writing multiple design units.

[Default=false]

-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_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 spruce_settings.param, if no prefix is specified.

-verbose

Triggers copious logging output.

[Default=false]

-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]

See also

-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”

See also

-excipient_codes

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

See also

-lipid_codes <codes>

Mechanism to define 3 letter codes that should be recognized as lipids if not done automatically, e.g. “PGR”, or “PGR,CHL”

See also

-make_packing_residues

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

[Default=true]

See also

-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]

See also

-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]

See also

-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]

See also

-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]

See also

-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]

See also

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

Build Parameters

-build_cterm_caps

Option to cap broken c-termini in protein chains

[Default=true]

See also

-build_nterm_caps

Option to cap broken n-termini in protein chains

[Default=true]

See also

-build_loops

Option to build loops for gaps in the protein structure

[Default=true]

See also

-build_sidechains

Option to build missing or partial protein sidechains

[Default=true]

See also

-enum_pockets

Option to detect pockets and generate design units from them

[Default=false]

Sidechain Build Parameters

-sc_delete_clashing_solvent

Option to allow build steps to remove clashing solvent

[Default=true]

See also

-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]

See also

-rot_library <value>

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

[Default=richardson2016]

See also

Loop Build Parameters

-build_with_crystalpacking

Include packing residues when building loops

[Default=false]

See also

-loop_db_filename <filename>

Database containing loop templates

See also

-crop_length <value>

Anchor residues on the protein to crop back for a better fit, results in longer loops being built

[Default=1]

See also

-transform_threshold <value>

Number of loops to allow through the sidechain clash checker. No matter this number, will process all with an identical sequence to target.

[Default=25]

See also

-strict_proline_match

Fuzzy matches in the loop database have to have proline in exact locations of sequence.

[Default=true]

See also

-loop_distance_buffer <value>

Fuzzy matches in the loop database has to have distance between anchor atoms correct, +/- buffer distance

[Default=1.0]

See also

-bb_clash_threshold <value>

Loops from the database where more than the threshold fraction of the backbone atoms clash, are rejected

[Default=0.25]

See also

-loop_clash_threshold <value>

Loops from the database where more than the threshold fraction of the loops atoms in addition to the backbone clashing ones clash, are rejected

[Default=0.2]

See also

-opt_shell <value>

Include atoms within this distance in the loop optimization, larger distance results in slower optimization

[Default=15.0]

See also

-opt_tolerance <value>

Tolerance for the loop optimization, smaller numbers result in slower optimization

[Default=0.001]

See also

-opt_stage1_iter_multiplier <value>

Number of steps per number of residues in the loop for the first stage optimizer

[Default=5]

See also

-opt_stage2_iter_multiplier <value>

Number of steps per number of residues in the loop for the second stage optimizer

[Default=10]

See also

-incl_solvation <value>

Include simple solvation model when building loops

[Default=true]

See also

-incl_SA_term <value>

Include solvent accessible surface area term when ranking the loops

[Default=true]

See also

-max_eval_loops <value>

Maximum number of loops to connect and minimize

[Default=5]

See also

-build_disulfidebridges <value>

Allow the loop builder to build disulfide brides during loop modeling (if possible)

[Default=true]

See also

-build_tails

Option to build missing terminal residues from sequence database

[Default=false]

See also

-seqalign_gap_penalty <value>

Gap penalty for sequence alignment during loop building

[Default=-10]

See also

-seqalign_extend_penalty <value>

Gap extension penalty for sequence alignment during loop building

[Default=-2]

See also

-reject_clashing_loops_postminimization

Reject loops that clash after minimization

[Default=true]

See also

-delete_existing_residues

Delete existing residues in the loop region before building

[Default=false]

See also

Cap Build Parameters

-cap_delete_clashing_solvent

Option to allow build steps to remove clashing solvent

[Default=true]

See also

-allow_truncate

Option to allow terminal residue to converted to cap, if cap will otherwise clash

[Default=true]

See also

Prep Parameters

-charge_radii

Option to assign partial charge and radii

[Default=true]

See also

-protonate

Option add and optimize protons in the system

[Default=true]

See also

-strict_protonate

Option to use strict protonation, disabling tautomer generation for heterogens

[Default=false]

Protonation Parameters

-generate_tautomers

Option to generate and use tautomers in the hydrogen network optimization

[Default=true]

See also

-het_group_nbr_dist <value>

Distance between heterogens used to determine optimization clusters for protonation

[Default=3.5 (angstroms)]

See also

-opt_expt_protons

Option to optimize hydrogens assigned in the experiment.

[Default=false]

See also

-flip_bias_scale

Bias scale for flippable groups (e.g. HIS/ASN/GLN) during hydrogen placement

[Default=1.0]

See also

Biological Unit Extraction Parameters

-bu_superpose

Option to superpose the biological units

[Default=false]

See also

-max_bu_atoms

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

[Default=50,000]

See also

-max_bu_parts

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

[Default=24]

See also

-min_align_score

Option to specify minimum sequence alignment score

[Default=200]

See also

-pref_author_record

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

[Default=true]

See also

Enumerate Pocket Parameters

-pocketMask

Option to set the subset of design unit components to be used for pocket finding. Multiple components can be combined as a comma separated string to create the input.

[Default=true]

-min_pocket_surf_area

Option to set minimum surface area of detected pocket.

[Default=150.0]

See also

-max_pocket_surf_area

Option to set maximum surface area of detected pocket.

[Default=3000.0]

See also

-pocket_burial_factor

Option to set the factor used to distinguish pockets from the general surface.

[Default=1.4]

See also

OEReceptor Parameters

-targetMask

Subset of design unit components to be used as target for the receptor. Multiple components can be combined as a comma separated string to create the input

[Default=protein,nucleic,cofactors,metals,lipids,other_proteins,other_nucleics,other_ligands,other_cofactors]

Please see more details at SPRUCE and ReceptorInDU.

Special Parameters

-no_prep

Option to skip all preparation steps. This will supersede any other optional flags set.

[Default=false]

Filter Options Parameters

-allow_filter_error

Option to allow running spruce prep even when structure fails spruce filter.

[Default=false]

-fix_res_names

Option to fix incorrect residue names.

[Default=true]

See also

-fix_res_states

Option to fix incorrect residue states.

[Default=true]

See also

-fix_bonds_to_metals

Option to fix incorrect covalent bonds to metals.

[Default=true]

See also

-fix_bb_atoms

Option to fix protein backbone atom states.

[Default=true]

See also

-fix_float_res

Option to delete floating residues

[Default=true]

See also

-fix_chainID

Option to fix missing chain ID

[Default=true]

See also

-fix_covalent_bond

Option to fix incorrect covalent bonds to halogens

[Default=true]

See also

-allow_validation_error

Option to allow writing OEDesignUnits even if they fail validation

[Default=true]