rk.refine

Run refinement with ROCKET

Running refinement with ROCKET is simple:

rk.refine config.yaml

The config.yaml file is a human readable/editable config file with all parameters included. And rk.preprocess will automatically generate two config files for you separately for phase1 run and phase2 run.

A typical config file is:

note: phase1_<your_note_here>
data:
  datamode: xray                   # xray or cryoem
  free_flag: R-free-flags          # free label flag in your mtz file
  testset_value: 1                 
  min_resolution: 3.0              # resolution cutoff 
  max_resolution: null
  voxel_spacing: 4.5   
  msa_subratio: null
  w_plddt: 0.0
  downsample_ratio: null           # int, downsample your large cryoem mtz files
paths:
  path: str                        # path to you working directory, should have ROCKET_inputs folder under that path
  file_id: str.                    # system id
  template_pdb: null               # relative path to your template pdb if you have
  input_msa: null 
  sub_msa_path: null
  sub_delmat_path: null
  msa_feat_init_path: null
  starting_bias: null              # Path to saved bias matrix
  starting_weights: null           # Path to saved weights matrix
  uuid_hex: d079fd4fd9             # Automatically generately hex id for run identification
execution:
  cuda_device: 0
  num_of_runs: 3
  verbose: false
algorithm:
  bias_version: 3
  iterations: 100
  init_recycling: 1
  domain_segs: null
  optimization:
    additive_learning_rate: 0.05        # Learning Rate for bias
    multiplicative_learning_rate: 1.0   # Learning Rate for weights
    weight_decay: 0.0001
    batch_sub_ratio: 0.7
    number_of_batches: 1
    rbr_opt_algorithm: lbfgs
    rbr_lbfgs_learning_rate: 150.0
    smooth_stage_epochs: 50
    phase2_final_lr: 0.001
    l2_weight: 1.0e-07
  features:
    solvent: true                 # Include solvent mask contribution
    sfc_scale: true               # Update scales per iteration
    refine_sigmaA: true           # Update sigmaA per iteration
    additional_chain: false
    bias_from_fullmsa: false
    chimera_profile: false

Check out the rk.config functionality to also generate default config files and modify them.