[modeller_usage] using model-loop-refine in Modeller9v1
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Subject: [modeller_usage] using model-loop-refine in Modeller9v1
From: "" <>
Date: Tue, 17 Apr 2007 16:49:01 +0800
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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