Loop Builder

Will build multiple loops in the specified region

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 Solvent Accessible Surface Area 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 Eistance 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
  • 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’)
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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
  • Optimize 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
  • Optimize 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
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • 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
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • 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