List of options
"-a", "--anom_weight"
"-b", "--anomalous_on" must be specified as: --anomalous_on 1 to keep Friedel pairs seperate in XSCALE
"-d", "--multiplicity_weight"
"-e", "--equilibrate_scales_to_R", Specify the expected low resolution Rmeas. GA will then run for a few cycles and find weights for the I/sigI weight automatically (TESTING)
"-f", "--find_files", Find files with the given pattern, make symbolic links and create a config file
"-g", "--generations", Number of generations
"-i", "--i_sigma_weight",
"-j", "--resolution_override", Override the resolution used during the GA optimization (normally all data)
"-k", "--CChalf_weight",
"-l", "--override_space_group", space group NUMBER
"-m", "--mutation_probability",
"-n", "--npop",
"-o", "--completeness_weight",
"-p", "--groups",
"-r", "--r_weight",
"-s", "--weighting_scheme",
"-x", "--crossover_probability",
"-y","--best_or_total" Optimises the total fitness across all groups in an individual OR just the best from all groups. "best" "total" or "total_with_garbage". The latter is for SIR, in which case the last group is not used for isomorphous differences.
--CChalf_mode default="overall" which CCHalf bin to use -- 'overall' or 'outer'")
--I_sigma_mode default="overall" which I over Sigma bin to use -- 'overall' or 'outer'")
--anom_mode default="AnoCC_overall" Anomalous mode -- 'SigAno_inner' or 'SigAno_overall' or 'AnoCC_inner' or 'AnoCC_overall' or 'AnoCC_resolution'"
--xscale_corrections keywords to be transferred to the XSCALE CORRECTIONS keyword
--output_resolution Can be a different resolution than the resolution used during the GA optimisation (usually higher)
--sir_iso_weight 100 wISO: weight of isomorphous terms vs intra dataset weights. Try 10,100,1000
--no_file_delete leaves temporary directories on disk. Required for SIR analysis
--explicit_random_seed Uses the specified random seed. Useful when comparing different CODGAS parameters (otherwise observed differences in outcomes could simply be due to different random seeds)
--sir_derivative_resolution_output truncate the derivative data in SIR. This can be useful to evade the SHELXC autoreindexing issue discussed elsewhere