On Sat, Jun 18, 2011 at 8:01 PM, flavio seixas
<oivalf_nix@yahoo.com> wrote:
Hi,
I had sucessfull modelled a protein without restrains.
However, when I put alpha helix restrains in the script below I face this problem:
File "model-restriction-single.py", line 21
rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:')))
^
IndentationError: unindent does not match any outer indentation level
I saw the script too many times and I am not able to see where the problem is.
Could anyone help-me?
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ()
env.io.hetatm = True
# 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
# Add some restraints from a file:
# Residues 47 through 57 should be an alpha helix:
rsr.add(secondary_structure.alpha(self.residue_range('47:', '57:')))
# Residues 130 through 140 should be an alpha helix:
rsr.add(secondary_structure.alpha(self.residue_range('130:', '140:')))
# Residues 182 through 184 should be an alpha helix:
rsr.add(secondary_structure.alpha(self.residue_range('182:', '184:')))
# Residues 191 through 195 should be an alpha helix:
rsr.add(secondary_structure.alpha(self.residue_range('191:', '195:')))
a = MyModel(env, alnfile='MODEL-TemplateA.ali',
knowns='TemplateA', sequence='MODEL',
assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 5
0
a.make()
# Get a list of all successfully built models from a.outputs
ok_models = filter(lambda x: x['failure'] is None, a.outputs)
# Rank the models by DOPE score
key = 'DOPE score'
ok_models.sort(lambda a,b: cmp(a[key], b[key]))
# Get top model
m = ok_models[0]
print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[1]
print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[2]
print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[3]
print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key])
m = ok_models[4]
print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key])
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