and I tried a model using the below specified script.
from modeller import * from modeller.automodel import * #from modeller import soap_protein_od
env = Environ() env.io.hetatm = True env.io.water = True class MyModel(AutoModel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: rsr.add(secondary_structure.Alpha(self.residue_range('111:A', '123:A'))) rsr.add(secondary_structure.Alpha(self.residue_range('646:B', '658:B')))
a = MyModel(env, alnfile='alignment.ali', knowns='SAM_docked', sequence='EGR', assess_methods=(assess.DOPE, #soap_protein_od.Scorer(), assess.GA341))
a.starting_model = 1 a.ending_model = 1 a.make()
The modelled structure generated without any error containing ion and water. But only two atoms were observed in the modelled structure but the ligand in the template contains 38 atoms. The atoms in ligand were not retained in the model from the template.
Please provide me with suggestions to solve this error?