---

From:  "" <jinlian05@lzu.cn>
Reply-To:  jinlian05@lzu.cn
To:  modeller_usage@salilab.org
Subject:  [modeller_usage] using model-loop-refine in Modeller9v1
Date:  Tue, 17 Apr 2007 16:49:01 +0800
>Hi,
>I am new to modeller and I have trouble creating a homology model of a
>protein using model-loop-refine. I modified the model-loop-refine.py script as
>shown below and I got error messages. I would appreciate it if any one
>can give me any suggestion.
>Thanks.
>
>from modeller import *
>from modeller.automodel import *
>
>log.verbose()
>env = environ()
>
>env.io.atom_files_directory = './:../atom_files'
>
># Create a new class based on 'loopmodel' so that we can redefine
># select_loop_atoms
>class myloop(loopmodel):
>     # This routine picks the residues to be refined by loop modeling
>     def select_loop_atoms(self):
>         return selection(self.residue_range('53:', '67:')
>                     (self.residue_range('89:', '96:')
>                     (self.residue_range('118:', '144:')
>                     (self.residue_range('166:', '177:')
>                     (self.residue_range('199:', '221:')
>                     (self.residue_range('243:', '254:'))
>
>a = myloop(env,
>            alnfile  = 'seg.ali',      # alignment filename
>            knowns   = '1u19A',               # codes of the templates
>            sequence = 'mrg1',               # code of the target
>            loop_assess_methods=assess.DOPE) # assess each loop with DOPE
>a.starting_model= 1                 # index of the first model
>a.ending_model  = 1                 # index of the last model
>
>a.loop.starting_model = 1           # First loop model
>a.loop.ending_model   = 2           # Last loop model
>
>a.make()                            # do modeling and loop refinement
>
>This is the error:
>   File "model-loop-refine.py", line 21
>     m = myloop(env,
>     ^
>SyntaxError: invalid syntax
>
>
>
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