Re: [modeller_usage] Trouble with angle restrain in chimera

[virginia miguel <>]

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 <> escribió:

De: João Rodrigues <>
Asunto: Re: [modeller_usage] Trouble with angle restrain in chimera
Para: "virginia miguel" <>
Cc: 
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" <> 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



https://salilab.org/mailman/listinfo/modeller_usage



-----Adjunto en línea a continuación-----

_______________________________________________
modeller_usage mailing list

https://salilab.org/mailman/listinfo/modeller_usage