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”, 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.

-add_receptors

Option to add OEReceptors onto the design units

[default = true]

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.

-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”

-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”

-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)
sitehopper	Superposition based on binding site similarities (sitehopper)

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_loops

Option to build loops for gaps in the protein structure

[default = true]

-build_sidechains

Option to build missing or partial protein sidechains

[default = true]

-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]

-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]

Loop Build Parameters

-build_with_crystalpacking

Include packing residues when building loops

[default = false]

-loop_db_filename <filename>

Database containing loop templates

-crop_length <value>

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

[default = 1]

-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]

-strict_proline_match

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

[default = true]

-loop_distance_buffer <value>

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

[default = 1.0]

-bb_clash_threshold <value>

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

[default = 0.25]

-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]

-opt_shell <value>

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

[default = 15.0]

-opt_tolerance <value>

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

[default = 0.001]

-opt_stage1_iter_multiplier <value>

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

[default = 5]

-opt_stage2_iter_multiplier <value>

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

[default = 10]

-incl_solvation <value>

Include simple solvation model when building loops

[default = true]

-incl_SA_term <value>

Include solvent accessible surface area term when ranking the loops

[default = true]

-max_eval_loops <value>

Maximum number of loops to connect and minimize

[default = 5]

-build_disulfidebridges <value>

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

[default = true]

Cap Build Parameters

-cap_delete_clashing_solvent

Option to allow build steps to remove clashing solvent

[default = true]

-allow_truncate

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

[default = true]

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]

-flip_bias_scale

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

[default = 1.0]

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]

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]

..option:: -min_pocket_surf_area

Option to set minimum surface area of detected pocket.

[default = false]

..option:: -max_pocket_surf_area

Option to set maximum surface area of detected pocket.

[default = false]

..option:: -pocket_burial_factor

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

[default = 1.4]

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]

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]

-fix_res_states

Option to fix incorrect residue states.

[default = true]

-fix_bonds_to_metals

Option to fix incorrect covalent bonds to metals.

[default = true]

-fix_bb_atoms

BRIEF Option to fix protein backbone atom states.

[default = true]

-fix_float_res

BRIEF Option to delete floating residues

[default = true]

-fix_chainID

BRIEF Option to fix missing chain ID

[default = true]

-fix_covalent_bond

BRIEF Option to fix incorrect covalent bonds to halogens

[default = true]

-allow_validation_error

Option to allow writing OEDesignUnits even if they fail validation

[default = true]