rk.config

Generate ROCKET default configuration files.

This generates YAML files with default ROCKET parameters to be used in refinement.

We have tested to find a set of good defaults, but this is where you could modify specific parameters like the learning rate or number of iterations if you wanted to experiment.

options:
  -h, --help            show this help message and exit
  --mode {phase1,phase2,both}
                        Execution mode: phase1, phase2, or both (default: both)
  --datamode DATAMODE   Data mode: xray, cryoem
  --working-dir WORKING_DIR
                        Working directory path (required)
  --file-id FILE_ID     File ID to use
  --pre-phase1-config PRE_PHASE1_CONFIG
                        Path to pre-phase1 configuration file (required for phase2 mode)

Typical command example:

rk.config --mode both --datamode xray --working-dir WORKING_DIR --file-id FILE_ID