Hi everyone,
I am trying to build a chimera protein based on two known structures that do not overlap, and I am trying to specify an angle restrain between the two domains that are model to give information of their relative orientation obtained experimentally using this script:
# Homology modeling with multiple templates
from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files env.io.atom_files_directory = './:../atom_files'
class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms f = forms.gaussian(group=physical.angle, feature=features.angle(a['CA:796'], a['CA:822'], a['CA:855']), mean=2.827, stdev=0.010) rsr.add(f)
a = MyModel(env, alnfile = 'align2.ali', # alignment filename knowns = ('2OK2','1FW6','1E3M'), # codes of the templates sequence = 'PAOI') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make()
but I get this error:
File "model-multiple.py", line 12, in ? class MyModel(automodel): File "model-multiple.py", line 21, in MyModel rsr.add(f) NameError: name 'rsr' is not defined
So I do not know what I am missing....if someone can help me!
Thank you in advance! Virginia.
I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)