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.