[modeller_usage] DOPE calculation for multiple models

Hi all,

I am trying to calculate the DOPE energy terms for multiple models. I know very
little about python and I'm not sure how to tell modeller to calculate the
energy for *each* model. I've attached my script to this e-mail - it's the last
4 lines of the script that I'm having difficulties with.  I'd be very grateful
if someone could point me in the right direction please?

Many thanks,

Yalini

-- 
Yalini Arinaminpathy, DPhil (Oxon)
Department of Molecular Biophysics and Biochemistry
Bass 426, 266 Whitney Avenue
Yale University
New Haven, CT 06520
(o): +1-203-432-8771
(f): +1-203-432-6946
(w): http://homes.gersteinlab.org/people/yalini/

from modeller import *
from modeller.automodel import *

log.verbose()    # for debugging

env = environ(rand_seed=-12312) # random seed

env.io.atom_files_directory = '.'  # Working directory

def defsym(mdl, aln, seg1, seg2):
    """Constrain segments |seg1| and |seg2| to be identical"""
    for (set,seg) in [(2,seg1), (3,seg2)]:
        mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg,
                       atom_types='CA', selection_status='INITIALIZE',
                       selection_search='SEGMENT')
    mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False))


def makealpha(mdl, aln, residue_ids):
    """Enforce alpha-helical structure on |residue_ids|"""
    mdl.restraints.make(aln, restraint_type='ALPHA', residue_ids=residue_ids,
                        spline_on_site=False)


class mymodel(automodel):
    def special_restraints(self, aln):
        segs = [('1', '99'), ('100', '198'), ('199', '297'), ('298', '396')]
        for n in range(len(segs)):
            defsym(self, aln, segs[n-1], segs[n])

        makealpha(self, aln, ('5', '30'))  	#M1 region (consensus)
        makealpha(self, aln, ('40', '53')) 	#P region (jalview p/out)
        makealpha(self, aln, ('64', '95')) 	#M2 region (consensus)
        makealpha(self, aln, ('104', '129'))
        makealpha(self, aln, ('139', '152'))
        makealpha(self, aln, ('163', '194'))
	makealpha(self, aln, ('203', '228'))
        makealpha(self, aln, ('238', '251'))
        makealpha(self, aln, ('262', '293'))
	makealpha(self, aln, ('302', '327'))
        makealpha(self, aln, ('337', '350'))
        makealpha(self, aln, ('361', '392'))


a = mymodel(env,
            alnfile  = 'x_vs_y.ali',  # The alignment filename
            knowns   = ('template'),  # The structure filenames, the pdb
                                     # is called filename.atm
            sequence = 'target')      # The sequence filename
a.starting_model= 1                  # Starting and ending model indices
a.ending_model  = 4
a.deviation = 4.0                    # Deviation in models

# Call the routine model which in turn calls all the other routines required.
a.make()

mdl = model(env, file = ???)
mdl.energy()
molpdf = mdl.energy(output='VERY_LONG', residue_span_range=(1,9999), normalize_profile=True, edat=energy_data(dynamic_sphere=True))
mdl.seq_id = 90.00
score = mdl.assess_ga341()