Re: [modeller_usage] help--model-segment.py

[Modeller Caretaker <>]

 wrote:
> Hi:
>   I want to use a part structure of template which belongs GPCR family. I write
> 'model-segment.py' scripts to model, the following is the scripts:
>
> from modeller import *
> log.verbose()
> class mymodel(automodel):
>   def selection_atoms(self):
>       self.pick_atoms(selection_segment=('37:A','63:A'),
>                       selection_search='segment',pick_atoms_set=1,
>                       res_types='all',atom_types='all',
>                       selection_from='all',selection_status='initialize')
>       self.pick_atoms(selection_segment=('74:A','96:A'),
>                       selection_search='segment',pick_atoms_set=2,
>                       res_types='all',atom_types='all',
>                       selection_from='all',selection_status='initialize')
>       self.pick_atoms(selection_segment=('111:A','133:A'),
>                       selection_search='segment',pick_atoms_set=3,
>                       res_types='all',atom_types='all',
>                       selection_from='all',selection_status='initialize')
>       self.pick_atoms(selection_segment=('153:A','173:A'),
>                       selection_search='segment',pick_atoms_set=4,
>                       res_types='all',atom_types='all',
>                       selection_from='all',selection_status='initialize')
>       self.pick_atoms(selection_segment=('203:A','224:A'),
>                       selection_search='segment',pick_atoms_set=5,
>                       res_types='all',atom_types='all',
>                       selection_from='all',selection_status='initialize')
>       self.pick_atoms(selection_segment=('250:A','274:A'),
>                       selection_search='segment',pick_atoms_set=6,
>                       res_types='all',atom_types='all',
>                       selection_from='all',selection_status='initialize')
>       self.pick_atoms(selection_segment=('287:A','308:A'),
>                       selection_search='segment',pick_atoms_set=7,
>                       res_types='all',atom_types='all',
>                       selection_from='all',selection_status='initialize')
> env=environ()
> env.io.atom_files_directory='./:../atom_files'
> env.edat.nonbonded_sel_atoms=2
> a=mymodel(env,
>           alnfile='1u19-tm.ali',
> 	  knows='1u19',
> 	  sequence='mrg-tm')
> a.starting_model=1
> a.ending_model=1
> a.make()  
>
> But when I run the mod9v1, there appears some errors:
> Traceback (most recent call last):
>   File "model-segment.py", line 3, in ?
>     class mymodel(automodel):
> NameError: name 'automodel' is not define
> How to define the 'automodel', please?

Please see http://salilab.org/modeller/9v1/manual/node22.html for an 
example. You have three problems with the script above:
1. You need to 'import' the automodel class, which is done in the 
example script with
from modeller.automodel import *

2. You can't name the selection method 'selection_atoms'. It has to be 
called select_atoms.

3. There is no pick_atoms method; you have to return a selection object. 
 In your case, something like
return selection(self.residue_range('37:A', '63:A'),
                 self.residue_range('74:A', '96:A'),
                 self.residue_range('111:A', '133:A'),
                 self.residue_range('153:A', '173:A'),
                 self.residue_range('203:A', '224:A'),
                 self.residue_range('250:A', '274:A'),
                 self.residue_range('287:A', '308:A'))

should be suitable.

	Ben Webb, Modeller Caretaker
--
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