Hey Virginia,
You have one less indentation level in that line. Python then considers it out of the class MyModel and thus, rsr is not previously declared. Just hit tab/4 spaces behind rsr.add and it should work.
Best,
João No dia 3 de Set de 2012 22:45, "virginia miguel" virgimiguel@yahoo.com.ar escreveu:
> 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) > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >