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!!