This example LINUS run file contains all the available options with annotation.

Make a copy of this file in your working directory and edit appropriately for your case.

from pylinus_2_4 import linusSim, ran

def gen_seeds():
    from random import uniform
    s1 = long(uniform(1.0, ran.M1))
    s2 = long(uniform(1.0, ran.M1))
    s3 = long(uniform(1.0, ran.M1))
    s4 = long(uniform(1.0, ran.M2))
    s5 = long(uniform(1.0, ran.M2))
    s6 = long(uniform(1.0, ran.M2))
    return s1, s2, s3, s4, s5, s6

def run(file,seed=None,mlfile=None,wtsfile=None,msfile=None,
        pmsfile=None,distfile=None):
    if seed is None:
        gen = apply(ran.generator, gen_seeds())
    else:
        gen = apply(ran.generator, seed)

    sim = linusSim.Linus(file, gen)

    # Define the number of actual amino acids
    # (Subtract ACE and NME)
    NUMRES = sim.protein.num_residues-2

    # This MUST be left uncommented
    # Set mlfile either to None or the actual name as below
    sim.load_movelist(mlfile)

    # Do not change anything above this line

    # This MAY be left uncommented
    # if msfile = None (see below) all mesostates will be Ck
    # or if msfile is defined below it will be loaded
    # or if use_ms_sampling=0 this will be ignored
    sim.load_mesostates(msfile)

    # Default conformational weights = "smart move set"
    sim.set_weights("helix", 0.25,"all")
    sim.set_weights("strand", 0.25,"all")
    sim.set_weights("turn1", 0.125,"all")
    sim.set_weights("turn2", 0.125,"all")
    sim.set_weights("coil", 0.25,"all")

    # Next command is only necessary if above do not total 1.0
    sim.normalize_weights()
    # Turn this on by defining pmsfile below
    if pmsfile is not None:
        sim.load_pmeso_weights(pmsfile)

    # Turn this on by defining distfile below
    if distfile is not None:
        sim.load_dist_const(distfile)

    # Turn this on by definging weights file below
    if wtsfile is not None:
        sim.read_weights_from_file(wtsfile)

    # with the following use_[flag]'s set to zero a default
    # pylinus simulation will be run
    # if you turn on some of the use_[flags]'s you may have to 
    # define the appropriate file below
    sim.set_simulation_parameters(numsave=100,
                                  beta=2.0,
                                  trials=1,
                                  reset_conformation=0,
                                  reset_emin_struc=0,
                                  updateweights=0,
                                  updatepmeso=0,
                                  use_lock_ss=0,
                                  use_pms_sampling=0,
                                  use_msd_sampling=0,
                                  use_ms_sampling=0,
                                  use_local_mov=0,
                                  use_dist_constraints=0,
                                  write_rc=0,
                                  numcycle=5000)
    sim.set_hbond_parameters(use_hbond=1,
                             hbond_score_short=0.4,
                             hbond_score_long=1.0,
                             hbond_winmax=NUMRES,
                             use_sidechain_hbond=1)
    sim.set_contact_parameters(use_contact=1,
                               contact_winmax=NUMRES)

    sim.run()

if __name__ == "__main__":
    try:
        import psyco
    except ImportError:
        pass
    else:
        psyco.bind(run)  
    import sys, os
    filename = sys.argv[1]
    file = os.path.basename(filename)

    # Only one of the following two lines uncommented
    mlfile = None
#   mlfile = os.path.abspath('movelist')

    # Only one of the following two lines uncommented
    wtsfile = None
#   wtsfile = os.path.abspath('weights')

    # Only one of the following two lines uncommented
    msfile = None
#   msfile = os.path.abspath('mesostates')

    # Only one of the following two lines uncommented
    pmsfile = None
#   pmsfile = os.path.abspath('pmeso_weights')

    # Only one of the following two lines uncommented
    distfile = None
#   distfile = os.path.abspath('noe.tbl')

    basedir = os.getcwd()
    for i in range(1):
        curdir = basedir + os.sep + 'sim_all'
        os.mkdir(curdir)
        os.link(filename, curdir+os.sep+file)

        # if any of these files are defined above uncomment the line
#       os.link('movelist', curdir+os.sep+'movelist')
#       os.link('weights', curdir+os.sep+'weights')
#       os.link('mesostates', curdir+os.sep+'mesostates')
#       os.link('pmeso_weights', curdir+os.sep+'pmeso_weights')
#       os.link('noe.tbl', curdir+os.sep+'noe.tbl')

        os.chdir(curdir)
        run(file,mlfile=mlfile,wtsfile=wtsfile,msfile=msfile,
            pmsfile=pmsfile,distfile=distfile)