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[modeller_usage] Modeller produces primary structure only



Dear all,

I tried to model part of my missing protein from a template but i fail to get proper structure (its just a linear line of amino acids) even though i followed the tutorial 100%.

My script (it is properly spaced in my file):

from modeller import *
from modeller.automodel import *    

log.verbose()
env = environ()
env.io.atom_files_directory = ['.', './template_struc']
env.io.hetatm = True
env.io.water = True

class MyModel(automodel):
def select_loop_atoms(self):
return selection(
self.residue_range('1154', '1298'))

a = MyModel(env, alnfile = 'alignment.ali',
knowns = '5xwp', sequence = 'sequence',
          assess_methods=(assess.DOPE,
                                           assess.GA341))

a.starting_model = 1
a.ending_model = 1000
a.make()

Alignment was proper and i checked every missing residue one by one. Dope scores are negative, GA scores 1.00). My templates are in /template_struc and this was tested to be working when i produced .ali files for my templates.

So whats the problem?

sincerely,

D.B.