Setting up the parameter file

Note

You can find a ready-to-use parameter file named

params_refine.py

in the tutorial directory.

The file is in the Python format and contains the following content:

protocol = 'refine'

SA_schedule = [
    (100000,   10000),
    (30000,   10000),
    (20000,   10000),
    (10000,   10000)
]

traj_frame_period = 1
print_frame_period = traj_frame_period

print_log_scores_to_files = True
print_log_scores_to_files_frame_period = 10

print_total_score_to_files = True
print_total_score_to_files_frame_period = 10

struct_resolutions = [0,10]
missing_resolution = 0
add_rbs_from_pdbs = False
connectivity_restraint_weight = 1.
conn_first_copy_only = False

rb_max_rot = 0.0174533
rb_max_trans = 1

add_symmetry_constraints = True
add_symmetry_restraints = True

add_xlink_restraints = True
x_xlink_score_type = 'LogHarmonic'
x_min_ld_score = 25
x_weight = 5000.0
x_xlink_distance = 15

ev_restraints = [
    {
        'name': 'ev_restraints_lowres',
        'weight': 10,
        'repr_resolution': 10
    }
]

scoring_functions = {
    'score_func_lowres': {
        'restraints': [
            'xlink_restraints',
            'conn_restraints',
            'ev_restraints_lowres',
            'FitRestraint',
            'sym_restraints'
        ]
    }
}

score_func = 'score_func_lowres'

ntasks = 1
cluster_submission_command = 'sbatch'
from string import Template
run_script_templ = Template("""#!/bin/bash
#
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=$ntasks
#SBATCH --mem-per-cpu=2000
#SBATCH --job-name=${prefix}fit
#SBATCH --time=00:30:00
#SBATCH -e $outdir/logs/${prefix}_err.txt
#SBATCH -o $outdir/logs/${prefix}_out.txt

echo "Running on:"
srun hostname

$cmd

wait
""")

To generate this file yourself from scratch:

Download the template parameter file (params_refine.py) from: https://git.embl.de/kosinski/Assembline/-/tree/master/doc/templates
Open the file in an editor to adjust the parameters