Hi: I want to use a part structure of template which belongs GPCR family. I write 'model-segment.py' scripts to model, the following is the scripts:
from modeller import * log.verbose() class mymodel(automodel): def selection_atoms(self): self.pick_atoms(selection_segment=('37:A','63:A'), selection_search='segment',pick_atoms_set=1, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('74:A','96:A'), selection_search='segment',pick_atoms_set=2, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('111:A','133:A'), selection_search='segment',pick_atoms_set=3, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('153:A','173:A'), selection_search='segment',pick_atoms_set=4, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('203:A','224:A'), selection_search='segment',pick_atoms_set=5, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('250:A','274:A'), selection_search='segment',pick_atoms_set=6, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') self.pick_atoms(selection_segment=('287:A','308:A'), selection_search='segment',pick_atoms_set=7, res_types='all',atom_types='all', selection_from='all',selection_status='initialize') env=environ() env.io.atom_files_directory='./:../atom_files' env.edat.nonbonded_sel_atoms=2 a=mymodel(env, alnfile='1u19-tm.ali', knows='1u19', sequence='mrg-tm') a.starting_model=1 a.ending_model=1 a.make()
But when I run the mod9v1, there appears some errors: Traceback (most recent call last): File "model-segment.py", line 3, in ? class mymodel(automodel): NameError: name 'automodel' is not define How to define the 'automodel', please? thanks a lot!!