Trouble with angle restrain in chimera
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)
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 >
participants (2)
-
João Rodrigues -
virginia miguel