Loop Builder

Will build multiple loops in the specified region

Main Parameters

Parameter Name

Loop backbone clash threshold

Option to build disulfide bridges

Build missing tails

Loop builder include crystal packing

Loop crop length

C-Terminal Bonding Residue

Delete clashing solvent

Extended Log Field

Include SA term

Include solvation

Log Field

Loop clash threshold

Loop anchor atom distance buffer

Loop Sequence

Number of loops to minimize and evaluate

N-Terminal Bonding Residue

Loop optimization shell

Opt stage 1 step/residue multiplier

Opt stage 2 step/residue multiplier

Loop optimization tolerance

Rotamer Coverage %

Rotamer Library

Enforce proline positions in loop templates

Number to transform

Related Cubes

Calculation Parameters

  • Loop backbone clash threshold (bb_clash_threshold) type: decimal: Loops from the database where more than the threshold fraction of the backbone atoms clash, are rejected.
    Default: 0.25
  • Option to build disulfide bridges (build_disulfidebridges) type: boolean: Allow the loop builder to build disulfide bridges during loop modeling (if possible).
    Default: True
  • Build missing tails (build_tails) type: boolean: Option to build missing tails (if information is available to do so)
    Default: False
  • Loop builder include crystal packing (build_with_crystalpacking) type: boolean: Include packing residues when building loops.
    Default: False
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Loop crop length (crop_length) type: integer: Anchor residues on the protein to crop back for a better fit, results in longer loops being built.
    Default: 1
  • C-Terminal Bonding Residue (cterm_res_string) type: string: Single site protein residue on to which the N-terminus of the loop attaches. Format ‘name:num:insert:chain[:fragno:altloc]’. e.g. ‘VAL:309: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard, but these should be avoided to ensure only one residue is selected.
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Delete clashing solvent (delete_clashing_solvent) type: boolean: Option to allow build steps to remove clashing solvent.
    Default: True
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Include SA term (incl_SA_term) type: boolean: Include solvent accessible surface area term when ranking the loops.
    Default: True
  • Include solvation (incl_solvation) type: boolean: Include simple solvation model when building loops.
    Default: True
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Loop clash threshold (loop_clash_threshold) type: decimal: Loops from the database where more than the threshold fraction of the loops atoms in addition to the bacbkone clashing ones clash, are rejected.
    Default: 0.2
  • Loop anchor atom distance buffer (loop_distance_buffer) type: decimal: Fuzzy matches in the loop database has to have distance between anchor atoms correct, +/- buffer distance.
    Default: 1.0
  • A template loop database file (loop_input_file) type: file_in: (Optional) A template loop database file, if not specified built-in database will be used
  • Loop Sequence (loop_sequence) type: string: The loop protein sequence in 1-letter codes as a string (ex. ‘EDVAT’)
  • Number of loops to minimize and evaluate (max_eval_loops) type: integer: Maximum number of loops to connect and minimize.
    Default: 5
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • N-Terminal Bonding Residue (nterm_res_string) type: string: Single site protein residue on to which the C-terminus of the loop attaches. Format ‘name:num:insert:chain[:fragno:altloc]’. e.g. ‘SER:315: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard, but these should be avoided to ensure only one residue is selected.
  • Loop optimization shell (opt_shell) type: decimal: Include atoms within this distance in the loop optimization, larger distance results in slower optimizations.
    Default: 15.0
  • Opt stage 1 step/residue multiplier (opt_stage1_iter_multiplier) type: integer: Number of steps per number of residues in the loop for the first stage optimizer.
    Default: 5
  • Opt stage 2 step/residue multiplier (opt_stage2_iter_multiplier) type: integer: Number of steps per number of residues in the loop for the second stage optimizer.
    Default: 10
  • Loop optimization tolerance (opt_tolerance) type: decimal: Tolerance for the loop optimization, smaller numbers result in slower optimizations.
    Default: 0.001
  • Rotamer Coverage % (rot_coverage) type: decimal: Coverage of the rotamers returned from the library in percent.
    Default: 100.0
  • Rotamer Library (rot_lib) type: string: Rotamer library to use for side-chain building.
    Default: Richardson2016
    Choices: Dunbrack, Richardson, Richardson2016
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Enforce proline positions in loop templates (strict_proline_match) type: boolean: Fuzzy matches in the loop database have to have proline in exact locations of sequence.
    Default: True
  • Number to transform (transform_threshold) type: integer: 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

Field parameters

  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network

Parallel Loop Builder

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.
    Default: 1 , Min: 1, Max: 65535
  • Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0