Setting up the parameter file¶

Note

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

params.py

in the IR_asymmetric_unit_refinement/ directory in our git repository ScNPC_tutorial git repository.

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

from string import Template

protocol = 'refine'

        SA_schedule = [
            (100,   5000),
        ]

        do_ini_opt = False

        traj_frame_period = 100
        print_frame_period = traj_frame_period

        print_log_scores_to_files = False
        print_log_scores_to_files_frame_period = 10

        print_total_score_to_files = False
        print_total_score_to_files_frame_period = 10

        states = 1
        struct_resolutions = [1,10]
        add_missing = False
        missing_resolution = 1

        add_rbs_from_pdbs = True


        connectivity_restraint_weight = 1.
        max_conn_gap = None
        conn_first_copy_only = False

        rb_max_rot = 2
        rb_max_trans = 3

        add_symmetry_constraints = False
        add_symmetry_restraints = True
        symmetry_restraints_weight = 1

        add_xlink_restraints = False

        add_em_restr = True

        discrete_restraints_weight=10000

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

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

        score_func = 'score_func_lowres'

        # SLURM template, adjust to your cluster environment
        ntasks = 1
        cluster_submission_command = 'sbatch'
        run_script_templ = Template("""#!/bin/bash
        #
        #SBATCH --ntasks=$ntasks
        #SBATCH --mem-per-cpu=2000
        #SBATCH --job-name=${prefix}fit
        #SBATCH --time=10:00:00
        #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:

Copy the template parameter file from the manual (i.e. Assembline repository) to the current directory:
```
cp doc/templates/params_refine.py .
```
Open the file in an editor to adjust the parameters