Hi,

I am trying to model a heptamer (homomultimer), but the structure generated is wrong because there are many clashes and it looks completely different from the template. How can I solve this issue? Please, see my files and scripts below.

The .ali for the alignment was edited by repeating the sequence seven times and separating each sequence by "/"

>P1;name

Sequence:name::::::::

XXXXX/XXXXX/XXXXX/XXXXX*

The alignment script

from modeller import *

env = Environ()

aln = Alignment(env)

mdl = Model(env, file='template', model_segment=('FIRST:A','LAST:F'))

aln.append_model(mdl, align_codes='template', atom_files='template.pdb')

aln.append(file='target.ali', align_codes='target')

aln.align2d(max_gap_length=50)

aln.write(file='aligned.ali', alignment_format='PIR')

aln.write(file='aligned.pap', alignment_format='PAP')

The script to build the model

from modeller import *

from modeller.automodel import *

#from modeller import soap_protein_od

log.verbose()

# Override the 'special_restraints' and 'user_after_single_model' methods:

class MyModel(AutoModel):

def special_restraints(self, aln):

# Constrain the A and B chains to be identical (but only restrain

# the C-alpha atoms, to reduce the number of interatomic distances

# that need to be calculated):

s1 = Selection(self.chains['A']).only_atom_types('CA')

s2 = Selection(self.chains['B']).only_atom_types('CA')

s3 = Selection(self.chains['C']).only_atom_types('CA')

s4 = Selection(self.chains['D']).only_atom_types('CA')

s5 = Selection(self.chains['E']).only_atom_types('CA')

s6 = Selection(self.chains['F']).only_atom_types('CA')

self.restraints.symmetry.append(Symmetry(s1, s2, 1.0))

def user_after_single_model(self):

# Report on symmetry violations greater than 1A after building

# each model:

self.restraints.symmetry.report(1.0)

env = Environ()

# directories for input atom files

env.io.atom_files_directory = ['.', '../atom_files']

# Be sure to use 'MyModel' rather than 'AutoModel' here!

a = MyModel(env,

alnfile = 'aligned.ali' , # alignment filename

knowns = 'template', # codes of the templates

sequence = 'target',

assess_methods=(assess.DOPE)) # code of the target

a.starting_model= 1 # index of the first model

a.ending_model = 100 # index of the last model

# (determines how many models to calculate)

a.make() # do comparative modeling

# Get a list of all succesfully built models from a.output

ok_models = [x for x in a.outputs if x['failure'] is None]

# Rank the models by DOPE score

key = 'DOPE score'

if sys.version_info[:2] == (2,3):

ok_models.sort(lambda a,b: cmp(a[key], b[key]))

else:

ok_models.sort(key=lambda a: a[key])