João! Thank you very much for your help! that work out! Sorry to bother you again but now the error that appears is the following:

File "model-multiple.py", line 17, in special_restraints     feature=features.angle(a['CA:796'], TypeError: unsubscriptable object

For what i can understand it does not recognize a sequence of atoms in

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)

I have tried

feature=features.angle(a['CA:796', 'CA:822','CA:855']),

and

feature=features.angle(a 'CA:796', 'CA:822','CA:855' ),

but they did not worked. Do you know how could I fix this?

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)

--- El lun 3-sep-12, João Rodrigues anaryin@gmail.com escribió:

De: João Rodrigues anaryin@gmail.com Asunto: Re: [modeller_usage] Trouble with angle restrain in chimera Para: "virginia miguel" virgimiguel@yahoo.com.ar Cc: modeller_usage@salilab.org Fecha: lunes, 3 de septiembre de 2012, 17:24

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)

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