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.